Abstract: Desiccation cracking is a common soil natural phenomenon. Research on desiccation cracking has mainly focused on morphological characteristics in lab-based experiments. In this study, three-dimensional (3D) geometric crack structures were extracted using paraffin casting in the field and transient image processing. The influence of cracks on farmland water and nitrogen leaching was quantified using the Water Heat Carbon Nitrogen Simulator (WHCNS) model. The 3D structural characteristics of the cracks obtained by the laser scanner were as follows: average length per square meter = 4.58 m, average surface width = 5.72 mm, and average depth = 9.06 cm. WHCNS analysis showed that cracks increased nitrogen leaching (97.40%, traditional fertilizer; 256.43%, optimized fertilizer), and that traditional fertilizer application had a greater nitrate nitrogen leaching risk. Irrigation type did not affect nitrate leaching, but heavy rainfall increased the risk and led to an 83.61% annual leaching volume increase. Additionally, the WHCNS model was used to simulate the effects of fracture, fertilization, irrigation, and rainfall intensity on nitrate leaching. The results showed that cracks had a notable influence on nitrate nitrogen leaching using optimal and traditional fertilization methods, and optimized fertilization reduced nitrate nitrogen leaching. Precipitation intensity was a key factor affecting nitrogen leaching. In this study, the simulation only calculated the nitrate nitrogen leached to underground and ignored nitrogen runoff from heavy precipitation, reducing the effect of precipitation on nitrogen leaching; however, the timing and amount of fertilizer and precipitation should be considered together when managing fields, especially in the summer, when rainfall is concentrated. The simulation showed that irrigation did not affect nitrate nitrogen leaching, which may be related to irrigation intensity and the leaching soil layer (100 cm) set by the model. However, the basin irrigation amount simulated in this study could not leach nitrate nitrogen below the 100 cm soil layer, which may have contributed to the small differences between methods. Thus, sprinkling irrigation and optimized fertilization should be adopted in combination to take full advantage of the water and fertilizer saving methods.