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In Northeast China’s degraded croplands, nitrate (NO3−-N) leaching is the dominant pathway for fertilizer-nitrogen (N) loss, which presents an increasing threat to the quality of groundwater. Conservation tillage, defined as no-tillage (NT) and straw retention, is a widely adopted management strategy to maintain cropland fertility in the black soil (BS) regions. At present, however, the impact of shifting from conventional to conservation tillage on the vertical distribution and regulatory mechanisms of NO3−-N derived from applied fertilizer-N (FNO3) remains poorly understood. Based on a 12-year field experiment, we integrated 15N-tracing field monitoring with 15N-paired-labeling incubation to quantify the vertical migration of FNO3 into deep soil profiles, and specify the dominant processes regulating N retention and supply. Across the tested BS croplands, total NO3−-N production rates (4.06–6.58 mg N kg−1 soil day−1) were faster than their consumption rates (0.36–0.92 mg N kg−1 soil day−1), leading to a net accumulation of NO3−-N, and implying a potential for leaching of NO3−-N, from the perspective of substrate availability. The results of the field 15N micro-plot experiment also indicated that, by maize maturity in the first growing season, an average of 7.5% of FNO3 had migrated to the 80–100 cm soil layer. During the following two growing seasons, the maximum accumulation of FNO3 had shifted downward to 140–160 cm and 180–220 cm, respectively. Such a pattern, particularly in light of the increased extreme precipitation in the studied regions, raises clear concerns about NO3−-N leaching losses. Compared with conventional management, no-tillage with full-rate straw mulching decreased net rates of NO3−-N production from 6.22 to 3.14 mg N kg−1 soil day−1. This reduction resulted from a decline in the gross oxidation of NH4+-N to NO3−-N (from 6.39 to 3.70 mg N kg−1 soil day−1) and an increase in DNRA (from 0.35 to 0.85 mg N kg−1 soil day−1), which collectively delayed the downward transport of FNO3. Conservation tillage also increased the gross rate of heterotrophic nitrification (from 0.19 to 0.36 mg N kg−1 soil day−1) and its proportion relative to total nitrification (from 2.8% to 8.9%). Despite this shift, autotrophic nitrification remained the dominant process for NO3−-N production in the tested BS croplands, likely due to a pH constraint on heterotrophic nitrification. With the increasingly widespread promotion of conservation tillage for soil fertility improvement, heterotrophic nitrification warrants greater attention, particularly in BS regions where pH < 6.5 and C/N contents are relatively high. Collectively, our findings provide a scientific basis for tailoring tillage practices to maintain sustainable agriculture in Northeast China.