Straw debris and fermentation strains are difficult to mix together in the fertilizer manufacturing process of tomato stalks. In order to solve the problem, a vertical screw mixer was put forward and the kinetics analysis of stuffing material was carried out, and the mixing process in the mixer was analyzed numerically by DEM simulation and measurement. The results showed that the variation coefficient of mixing was less than 10% and the average power consumption was less than 0.0781kW after stirring for 3min, confirming the feasibility of the mixer in fertilizer manufacturing process of tomato stalks. The variation coefficient of mixing was decreased with the increase of pitch of blade, but the power consumption achieved the maximum at a medium pitch. With the increase of rotational speed, the variation coefficient of mixing was decreased as well, but the power consumption was increased substantially. With the increase of stuffing material height, variation coefficient of mixing and the power consumption were increased. The rank order for the effect on the variation coefficient of mixing from the most important to the least important was pitch of blade, rotational speed and stuffing material height. A mathematical model of variation coefficient of mixing with mixer geometrical variables and work parameters was built and optimized. The optimum variation coefficient for mixing was 43% when stuffing material height was 440mm, rotational speed was 30r/min and pitch of blade was 400mm. The simulated results were compared with the tested data, showing a 13.5% error between simulation and observation. This suggested that the simulated results were correct and revealed efficient mixing mechanism of the mixer. The study provides a theoretical basis for research and development of efficient and specific equipment in tomato straw and fermentation strains mixing.