An early settlement in the area of today's Blagoveshchensk was the Ducher town whose name was reported by the Russian explorer Yerofey Khabarov as Aytyun in 1652, as Aigun from 1683 to 1685, and as Aigun Old Town from 1685 until the massacre in 1900,[18] which is known to Russian archaeologists as the Grodekovo site, after the nearby village of Grodekovo about 25–30 km (16–19 mi) southeast of Blagoveshchensk.

[22][23] The series of conflicts between Russians and China ended with Russia's recognition of the Chinese sovereignty over both sides of the Amur by the Nerchinsk Treaty of 1689.

As the balance of power in the region had changed by the mid-19th century, the Russian Empire was able to take over the left (generally northern, but around Blagoveshchensk, eastern) bank of the Amur from China.

Local historians noted the pre-eminence of Blagoveshchensk in the economy of the late 19th century Russian Far East, which was reflected when the heir to the Russian throne, Nicholas Alexandrovich (the future Tsar Nicholas II), visited in 1891 during his grand tour of Asiatic Russia, and the locals presented him with bread and salt on a gold tray, rather than on a silver one as in other cities of the region.

[25] According to the Orthodox belief, the city was allegedly saved by a miraculous icon of Our Lady of Albazin, which was prayed to continuously during the shelling which lasted almost two weeks.

The plan, however, was vetoed by the governor, and the decision was made instead to take the deportees to the stanitsa of Verkhneblagoveshchenskaya—the place where the Amur is at its narrowest—and make them leave Russia there.

As the local ataman refused to provide boats to take them across the river (despite the orders of his superior), few of them made it to the Chinese side.

The rest drowned in the Amur, or were shot or axed by the police, Cossacks and local volunteers, if they refused to leave the bank.

Local Chinese memory holds that a massacre that took place then, at the hands of the Cossacks, which killed so many that the Amur River was choked.

He still remembers the massacre at Blagoveshchensk when nearly 8,000 unarmed men, women, and children were driven at the point of the bayonet into the raging Amur, until — as one of the Russian officers who participated in that brutal murder told me at Chin-Wang-Tao in 1900 — "the execution of my orders made me almost sick, for it seemed as though I could have walked across the river on the bodies of the floating dead."

Not a Chinaman escaped, except forty who were employed by a leading foreign merchant who ransomed their lives at a thousand roubles each.

From 1920 until 1922, the city was declared part of the Far Eastern Republic, an area which was nominally independent, but in reality, a buffer zone under control of the Russian SFSR.

During the Cultural Revolution in China, the city was subject to Maoist propaganda blasted from loudspeakers across the river 24 hours a day.

Blagoveshchensk is part of a free-trade zone which includes the Chinese city of Heihe, located on the other side of the Amur River.