To improve the quality of side deep fertilization in paddy fields and study the dynamic change in fertilizer particles in fertilizer boxes, a model connecting the mechanical components and fertilizer based on the discrete element method was established, and a numerical simulation analysis of the spiral fertilizer distributor was conducted with EDEM software. The primary factors affecting the uniformity and stability of the fertilizer were studied. Using an orthogonal experimental design and numerical simulation technology, the speed, lead and diameter of a steel wire were selected as experimental factors, the mean fertilization value and the fertilization coefficient of the variation were selected as evaluating indicators, a mathematical model between the factors and indicators was established by virtual orthogonal testing, and the numerical processing was optimized with Design-Expert 6.0.10 software. The results showed that the primary and secondary factors affecting the comprehensive performance occurred in the following sequence: steel wire speed > steel wire diameter > steel wire lead. When the speed, lead, and diameter of the steel wire were 15 r/min, 65 mm and 7 mm, respectively, the operation performance was superior. High-speed video camera analysis and bench tests showed that the results were consistent with the simulation optimization. The mean value and the coefficient of variation of fertilization were 9.39 g and 3.71%, respectively, which satisfy the agronomic requirements for paddy field side deep fertilization.