Under the modern manufacturing environment-oriented, both productivity and green environmental consideration are made in diverse phases of production operations. In this paper, in order to dynamically analyse and control changes of Work-In-Process (WIP) inventory level, a centralized fuzzy control method is proposed. Additionally, a new environmental management accounting method, Material Flow Cost Accounting (MFCA), is adopted to find and calculate environmental waste hiding in the production processes. Moreover, a simulation model integrated with these methods above is constructed. Based on the simulation data, sensitivity analysis between control factors of WIP inventory level and negative product costs ratio is made. To achieve a reasonable productivity as well as green environmental performance for this case, a corresponding optimized solving measure is put forward by means of OptQuest in the Arena simulation system. Through studying, the proposed control approach of WIP can reduce the green environmental cost, and improve production capacity.