Winter cover crops have been shown to promote the accumulation of microbial biomass carbon and nitrogen, enhance nutrient cycling, reduce erosion, improve ecosystem stability, etc. In the black soil area of Northeast China, Triticum aestivum L., Medicago sativa L., Vicia villosa Roth., Triticum aestivum L. and Medicago sativa L. mixed planting, Triticum aestivum L. and Vicia villosa Roth. mixed planting, and winter fallow fields (CK) were selected to investigate the effects of winter cover crops on soil total carbon and nitrogen and microbial biomass carbon and nitrogen. The results showed that (1) after seasonal freeze-thaw, the rate of change in SOC (−2.49~6.50%), TN (−1.54~5.44%), and C/N (−1.18~1.16%) was less than that in SMBC (−80.91~−58.33%), SMBN (−65.03~332.22%), and SMBC/SMBN (−45.52~−90.03%); (2) winter cover crops not only alleviated the negative effects of seasonal freeze-thaw, which reduces SMBC and qMBC, but also increased SMBN and qMBN; (3) there was an extremely significant (p < 0.01) positive correlation between SOC and TN, a significant (p < 0.05) negative correlation between SMBC and SMBN, and there was no significant correlation between SOC and SMBC or between TN and SMBN; (4) alkali-hydrolysable nitrogen had the greatest impact on SOC and TN, while the soil’s saturation degree had the greatest impact on SMBC and SMBN; and (5) the Triticum aestivum L. monoculture was the most effective in conserving soil microbial carbon and nitrogen. In conclusion, winter cover crops can mitigate the reduction in soil microbial biomass carbon caused by seasonal freeze-thaw and also increase the soil microbial nitrogen content in the black soil region of Northeast China, of which Triticum aestivum L. monoculture showed the best performance.