Abstract: Preferential flow is an important mechanism that relies on macropores for moisture to infiltrate into soil. Understanding this process affects the study of soil moisture, solute transport, and environmental protections for field management practices. In this study, a brilliant blue staining tracer field experiment and the soil water heat carbon nitrogen simulator (WHCNS) model were used to explore the effects of preferential flow of macropores on soil water transport and nitrate nitrogen leaching. The WHCNS model was used to simulate soil water and nitrogen migration through macropores in a North China Plain winter wheat-summer maize rotation field with heavy rainfall, fertilization, and irrigation. A dyeing tracer was used to follow water infiltration into no-tillage and rotary-tillage soil, and Pearson correlation coefficient analysis was performed on the stained area and the no-tillage soil stable infiltration rate. The results showed that the no-tillage soil infiltration depth and dyeing area were higher than that of the rotary-tillage soil. The no-tillage soil had a deeper dyeing depth, reaching 80–100 cm, while that of rotary-tillage was shallow, reaching only 15–20 cm. The no-tillage soil had a high degree of preferential flow and transported moisture to the deep-soil. There was no correlation between the no-tillage soil dyeing area and the stable infiltration rate (P = 0.68). Therefore, dye tracers cannot quantify the soil stable infiltration rate. At the same time, the WHCNS simulation results of nitrate nitrogen leaching in 0–100 cm soil layer showed that the presence of macropores increased the nitrate nitrogen leaching in both traditional and optimal fertilization modes, compared with no macropores. On the other hand, in the presence of macropores, optimized fertilization reduced nitrate nitrogen leaching by 46.0% compared with that in traditional fertilization. The sprinkler irrigation reduced leaching by 15.6% compared with that in conventional flood irrigation, and heavy rainfall increased leaching by 119.4%. If the farmland has macropores, organic fertilizer and sprinkler irrigation may be used to save water and reduce nitrate nitrogen leaching; however, increased leaching is expected during heavy rainfall. Therefore, climatic conditions should be considered when fertilizing to determine suitable irrigation amounts. This study used a field tracing experiment and WHCNS model simulation to demonstrate that preferential flow can increase soil water infiltration and nitrate nitrogen downward movement and provides guidance for optimizing farmland water and fertilizer management with macropores in the North China Plain.