In smart factory, automatic processing mode with high-tech content has become the main method of the modern sorting system. In small manufacturing enterprises, most of the warehouse sorting system is not done with automation but by manual labor. However, along with the increase in demand for products and the expansion of production scale, an automated warehouse sorting system is necessary. Automated sorting system is a typical discrete logistics system. Applying modern logistics simulation technology can help to analyze and evaluate the actual systems. In this paper, we take a small scale bag manufacturing enterprise for example, to design an automated sorting system in the warehouse. Applying discrete event simulation, model and simulate the system with the Automod as one of the most popular logistics simulation tools. Through conducting the experiments and analyzing the experimental results, verify the feasibility of our design and put forward the improvement of the system. The proposed method can provide the references for other small manufacturing enterprises and help business managers to make decisions.