- _Recollections of a Visit to the Philippines in the Year 1853_ (1853)
- _The Malay Archipelago: The Land of the Orang-Utan, and the Bird of Paradise. A Narrative of Travel, 1848-1862_ (2 vols., 1869)
- _Journal and Proceedings in the Straits of Korea_ (1869)
- _Borneo and the Indian Archipelago_ (1870)
- _The Travels and Adventures of Ferdinand Mendez Pinto, the Portuguese_ (1880)
- _Old Penang_ (1911)
- _The History of the Indian Archipelago_ (1911)
- _Narrative of the Earl of Elgin's Mission to China and Japan in the Years 1857, '58, '59_ (1912)
- _Reminiscences of Travel in the Far East_ (1913)
Articles:
- "Notices of Chinese Grammar" (_The Chinese Repository_, 1847)
- "Chinese Etiquette and Customs" (_The Chinese Repository_, 1847)
- "The Religion of China" (_The Chinese Repository_, 1847)
- "The Malay Piracies" (_The Journal of the Indian Archipelago and Eastern Asia_, 1847)
- "Notices of the Indian Archipelago and Malayan Ethnology" (_The Journal of the Indian Archipelago and Eastern Asia_, 1850)
- "The Chinese in Borneo" (_The Journal of the Indian Archipelago and Eastern Asia_, 1850)
- "The Bataks of Sumatra" (_The Journal of the Indian Archipelago and Eastern Asia_, 1851)
- "Some Account of the Banting Muruts" (_The Journal of the Indian Archipelago and Eastern Asia_, 1852)
- "The Birds of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1852)
- "The Mammalia of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1853)
- "The Reptiles of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1853)
- "The Fishes of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1853)
- "The Insects of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1853)
- "The Plants of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1854)
- "The Geology of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1855)
- "The Climate of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1856)
- "The Physical Geography of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1857)
- "The Ethnology of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1858)
- "The History of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1859)
- "The Literature of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1860)
- "The Arts and Sciences of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1861)
- "The Commerce of the Malay Archipelago" (_The Journal of the Indian Archipelago and Eastern Asia_, 1862)