This paper proposes an optimal design model of microgrids with small-scale photovoltaic systems (SS-PVs) and storage batteries for industries along with three economic evaluation indicators. The proposed indicators are levelized energy cost, emission reduction benefits, and payback period. They are combined to comprehensively evaluate economic performances and investment risk of the microgrids. The optimal model considering local solar insolation level, environment benefits, different operation modes, and initial investment costs is formulated and applied to obtain the optimal configuration of the microgrids with SS-PVs by particle swarm optimization (PSO) method. The simulation results based on 4-month real operation data of a 500-kW PV microgrid for industries in Guangdong, China, have verified that the optimal design by the proposed method can meet the technical requirements as well as the economic performances, thus effectively optimizing the microgrid with SS-PVs for industries in both economic and environmental aspects. Furthermore, the sensitivity analysis of the impact of different parameters on the system is also performed. The results provide a reference for the application of similar projects.