The city seat, Fuyuan Town, sits on the southern bank of the Amur.

The Bolshoy Ussuriysky Island (Heixiazi Island), partitioned between the two countries by the treaty of 2004, is in the city's northeastern corner, the mid-island border line running about 25 km (16 mi) east of Fuyuan Town.

Fuyuan has a humid continental climate (Köppen: Dwa) bordering on Dwb, with long, cold winters, but also dry, although less extreme than more inland locations of Heilongjiang.

[1] As of late 2013, schedule systems list one passenger train a day serving Fuyuan; it comes from Harbin via Jiamusi, covering 973 km (605 mi) in 17.5 hours.

[1] 2 Formally part of Oroqen Banner in Inner Mongolia but administered de facto by Daxing'anling Prefecture in Heilongjiang.