In command of , Heywood conducted a series of surveys of the eastern coasts of Ceylon and India, areas that had not been studied previously, and produced what Caroline Alexander describes as "beautifully drafted charts". In later years he was to produce similar charts for the north coast of Morocco, the River Plate area of South America, parts of the coasts of Sumatra and north-west Australia, and other channels and coastlines. His skill in this area may well have developed from Bligh's tutelage in the earlier stages of the Bounty voyage. Bligh, an accomplished draughtsman, had written of Christian and Heywood: "These two had been objects of my particular regard and attention, and I had taken great pains to instruct them." James Horsburgh, who was hydrographer to the East India Company, wrote that Heywood's work had "essentially contributed to making my Sailing Directory for the Indian navigation much more perfect than it would otherwise have been." The extent of Heywood's professional reputation was demonstrated when the position of Admiralty Hydrographer was offered to him in 1818, after he had retired from the sea. He declined, and the appointment went to Francis Beaufort on Heywood's recommendation.
Captain Heywood took command of HMS Dedaigneuse in April 1803 in the East Indies. On 14 December she captured the two (or four-gun) French privateer Espiegle. Because of his poor health and the death of his elder brother, Captain Heywood resigned his command on 24 January 1805. He then returned to the United Kingdom as a passenger on the East Indiaman .
Later service
After a brief period ashore in 1805–06 Heywood was appointed flag captain to Rear-Admiral Sir George Murray, aboard . In March 1802 Murray's squadron was employed in the transportation of troops from the Cape of Good Hope to South America, in support of a failed British attempt to capture Buenos Aires from the Spanish, who were allied to the French during the Napoleonic Wars. Polyphemus remained in the River Plate area, carrying out surveying and merchant vessel protection duties. Heywood was back in England in 1808, in command of , which in the following year was part of a squadron that attacked and destroyed three French frigates in the Bay of Biscay, an action for which he received the Admiralty's thanks. knowing that he had "perjured himself" in saying that he was kept below and therefore prevented from joining Bligh.|group=n She believes that Pasley and Graham may have bribed William Cole to testify that Heywood had been held against his will, echoing Thomas Bond, Bligh's nephew, who had asserted in 1792 that "Heywood's friends have bribed through thick and thin to save him". John Adams, the last survivor of Christian's Bounty party that sailed to Pitcairn Island, was discovered in 1808. In 1825, interviewed by Captain Edward Belcher, Adams maintained that Heywood was on the gangway, not below, and "might have gone [in the open boat] if he pleased." Two weeks later he married Frances Joliffe, a widow whom he had met ten years earlier, and settled with her at Highgate, near London. The couple had no children but, apart from his daughter in Tahiti, there is a suggestion in a will which he signed in 1810 that Heywood had also fathered a British child—the will makes provision for one Mary Gray, "an infant under my care and protection".
In May 1818, Heywood declined command of the Canadian Lakes with the rank of commodore. As he had become content with shore life, he said he would only accept another appointment in the event of war. In retirement Heywood published his dictionary of the Tahitian language, wrote papers relating to his profession, and corresponded widely. He enjoyed a circle of acquaintances which included the writer Charles Lamb, and was a particular friend of the hydrographer Francis Beaufort. He destroyed much of his writing shortly before his death, but a document from 1829 survives, in which he expresses his views on the unfitness for self-government of Greeks, Turks, Spaniards and Portuguese, the iniquities of the Greek Orthodox and Roman Catholic churches, and the doubtful benefits of Catholic emancipation in Ireland. Of strong religious convictions, Heywood was increasingly interested in spiritual matters during the last years of his life. His health began to fail in 1828, and he died after suffering a stroke, aged 58, in February 1831. He was interred in the vault of Highgate School chapel, where a memorial plaque was dedicated on 8 December 2008, and is also memorialised on the grave of his widow Frances on the west side of Highgate Cemetery.
Nessy Heywood had died on 25 August 1793, less than a year after Heywood's pardon.