In order to reveal the emission law of trace greenhouse gases from black soil paddy fields in cold regions and the relationship between trace greenhouse gas emission from paddy fields and water use efficiency and nitrogen absorption and utilization efficiency, two water management modes of dry wet alternate irrigation and traditional flooding irrigation and four biochar application levels (0t/hm2, 2.5t/hm2,12.5t/hm2 and 25t/hm2) were set. Compared with traditional flooding irrigation, 15N tracer technology was applied to study the seasonal variation of methane and nitrous oxide emissions from black soil paddy fields in cold regions under water biochar management, clarify the relationship between rice water and nitrogen utilization and methane and nitrous oxide emissions, and calculate the global warming potential (GWP) and emission intensity (GHGI) of greenhouse gases. The results showed that when the biochar application rate was the same, the methane emission flux of the traditional flooding irrigation mode was significantly higher than that of the dry wet alternate irrigation mode (P<0.05), while the nitrous oxide emission flux was lower than that of the dry wet alternate irrigation mode. The total emission of methane in the dry wet alternate irrigation mode was significantly lower than that in the traditional flooding irrigation mode (P<0.05), while the total emission of nitrous oxide was higher than that in the traditional flooding irrigation mode. The application of biochar had a significant effect on the emission reduction of methane and nitrous oxide in paddy fields. The GWP and GHGI of trace greenhouse gases in paddy fields under dry wet alternate irrigation mode were significantly lower than those under traditional flooding irrigation mode (P<0.05). The application of biochar could reduce the GWP and GHGI of trace greenhouse gases in paddy fields. The water use efficiency of dry wet alternate irrigation mode was significantly higher than that of traditional flooding irrigation mode (P<0.05). Proper application of biochar could increase the water use efficiency and the absorption and utilization rate of fertilizer as a whole, base fertilizer, tiller fertilizer and ear fertilizer. GWP and GHGI of trace greenhouse gases in paddy fields under the two irrigation modes were significantly negatively correlated with water use efficiency (P<0.05). GWP and GHGI of trace greenhouse gases in paddy fields under the two irrigation modes were significantly or extremely significantly negatively correlated with the absorption and utilization rate of fertilizer as a whole, base fertilizer, tiller fertilizer and panicle fertilizer.