In the late Middle Ages, the people living along the lower course of the Amur were collectively known in China as the "wild Jurchen". The Yuan Dynasty Mongols sent expeditions to this area with an eye toward using the region as a base for attack on Japan, or for defending against the Sakhalin Ainus. According to the History of Yuan, in 1264 the Nivkhs recognized the Mongol sovereignty. In 1263, the Mongols set up the "Command Post of the Marshal of the Eastern Campaign" near the modern settlement of Tyr, some upstream from today's Nikolayevsk-on-Amur. At roughly the same time, a shrine was built on the Tyr Rock. From 1411 to 1433, the MingeunuchYishiha, a man of Haixi Jurchen origin, led four large missions to win over the allegiance of the "Jurchen" tribes along the Sunggari and Amur Rivers. During this time, the Yongning Temple was constructed at Tyr, and stelae with inscriptions erected.
Russian period
The Russian settlement, likely preceded by the Manchu village of Fuyori, was founded as Nikolayevsky Post by Gennady Nevelskoy on 13 August 1850 and named for Tsar Nicholas I. The settlement quickly became one of the main economic centres on the Pacific coast of the Russian Empire. It became Russia's main Pacific harbour in 1855 after the Siege of Petropavlovsk of 1854. It was granted town status and renamed Nikolayevsk-on-Amur in 1856, when Primorskaya Oblast was established. Admiral Vasily Zavoyko supervised the construction of a naval base in Nikolayevsk-on-Amur. The town emerged as an important commercial harbour; however, due to navigational difficulties caused by the sandbanks in the Amur estuary and because sea ice made the harbour unusable for five months each year, the main Russian shipping activities in the Pacific transferred to the better situated Vladivostok in the early 1870s. The town remained the administrative centre of this region until 1880, when the governor relocated to Khabarovsk. Anton Chekhov, visiting the town on his journey to Sakhalin in 1890, noted its rapid depopulation, although this trend slowed somewhat in the late 1890s with the discovery of gold and the establishment of salmon fisheries. During the Russian Civil War of 1917-1922 the town's population plummeted from 15,000 to 2,000, as a local partisan leader, later executed by the same Bolsheviks he was supposed to be aligned with, razed the entire town to the ground and massacred the minority Japanese population along with most of the Russian population. Around 1940 a prison camp of the gulag system was located in the town. Like many other places in the Russian Far East, the town has seen a drop in population since the dissolution of the Soviet Union, dropping from 36,296 inhabitants recorded in the, to only 22,772 in 2010.
Nikolayevsk-on-Amur has a borderline humid continental climate, almost cold enough to be a subarctic climate. Precipitation is not as low in the winter as over most of Siberia since the coast in on the fringe of influence from the Aleutian Low. The near-maritime location only marginally—by —moderates the winters compared to interior Siberia, but makes the summers noticeably cool though the Oyashio fogs are less prevalent than on Sakhalin itself and sunshine hours therefore rather longer.