Changes in soil total nitrogen (N) content would affect wetland function and the global N cycle. Determination of spatial heterogeneity controlling factors of wetland soil total N content per unit mass is essential to assess responses of ecosystem N cycle to global change. However, such information is limited in permafrost zones because few soil profiles have been acquired and methods to predict spatial distributions of wetland soil total N content in large areas are inefficient, which increase uncertainty in evaluations of N cycle at national or global scales. To determine the spatial heterogeneity of wetland soil total N content at different soil depths and frozen zones and the factors controlling wetland soil total N content in the frozen zones of Northeast China, the spatial pattern of wetland soil total N content was investigated by using a random forest method that combined field samples with environmental factors. Vertically, wetland soil total N content decreased with increasing soil depth, with the highest content in the top soil layer (0–30 cm). Spatially, wetland soil total N content decreased from northwest to southeast, with relatively high total N content in a continuous permafrost zone and relatively low total N content in a seasonally frozen zone. The overall coefficient of variation of wetland soil total N content in the frozen zones of Northeast was 29.58 %, indicating moderate variation. Land surface temperature, mean annual temperature, and mean annual humidity significantly affected total N content in 0–30 and 30–60 cm soil layers, suggesting that variations in temperature and humidity altered sequestration processes of wetland soil total N content. In the 60–100 cm soil layer, compared with other environmental factors, mean annual humidity, altitude, and mean annual precipitation had the greatest influence on the spatial distribution of wetland soil total N content. The study unravels the spatial pattern of soil total N content in frozen zones of Northeast China and reflects the direct and indirect effects of environmental factors on total N content. This provides a basis for the management and protection of wetland ecosystems.