Distinguished features of cities influence the characteristics of CH4 emissions. A city-level emission inventory represents the characteristics of CH4 on a smaller scale, according to the special factors in each city. A city-level emission inventory was established to reveal the characteristics and source profile of CH4 emissions in the coldest province, which is a typical provincial cold region in northeast China. The dominant sources were identified for targeted cities. Rice cultivation, coal mining, oil and gas exploitation, and livestock are the dominant emission sectors. Emissions from other sectors, including wastewater disposal, biomass burning, landfill, etc. were also estimated. The provincial CH4 emissions increased gradually from 2003 to 2012, up to 2993.26 Gg with an annual increase rate of 2.85%; the emissions were 2740.63 in 2020. The emissions of CH4 in Harbin, Daqing, Jiamusi, and Hegang cities were higher than in the other nine cities, which were 337.23 Gg, 330.01 Gg, 328.55 Gg, and 307.42 Gg in 2020, respectively. Agriculture, including the rice cultivation, livestock, and biomass burning sectors contributed to 51.24–62.12% of total emissions, and the contributions increased gradually. Coal mining, oil and gas exploration, and fossil fuel combustion are energy-related sources, which contributed up to 37.91% of the total emissions, and the proportion kept decreasing to 23.87% in 2020. Furthermore, meteorological factors are especially relevant to the region, by which the differences of ambient temperature are over 60 °C (±30 °C). In the summer, CH4 emissions from the rice cultivation, biomass burning, livestock, and landfill sectors are obviously distinct from the heating period (winter), while few differences in CH4 emissions are found from wastewater disposal and the fossil fuel production sectors.