Intercropping improves yield and is broadly adopted worldwide; however, the risk and regulatory mechanism of nitrate leaching in intercropping compared with monocropping remain elusive. A fixed plot field experiment was conducted with three cropping patterns (maize monocropping, potato monocropping, and maize–potato intercropping) under four (nitrogen) N levels in Kunming, China during 2014–2017. Based on crop N uptake and soil nitrate transformation, the underlying mechanism of potential nitrate-N (NO₃⁻-N) leaching (NO₃⁻-N accumulation below the root layer) and N regulation was explored under intercropping and monocropping. The results showed that the area-scaled potential NO₃⁻-N leaching under intercropping was mitigated by 3.4–37.4%, with a mean of 15.8% relative to the weighted mean of maize- and potato-monocropping. Intercropping-related mitigation of potential NO₃⁻-N leaching was enhanced with increasing N level. Intercropping increased the ammonia-oxidizing archaea population and soil nitrification potential but had no significant impact on the abundance of ammonia-oxidizing bacteria and narG. Redundancy analysis and structural equation modeling indicated that soil water played a crucial role in regulating the intercropping-related mitigation of potential NO₃⁻-N leaching, while the improvement in N uptake by intercropped maize reduced the potential NO₃⁻-N leaching at low and medium N levels. The results highlight the intercropping advantage over monocropping in mitigating the risk of NO₃⁻-N leaching. This study provides insights into the environmental impacts of diversified cropping systems and regulating mechanisms.