As one of health industries, pharmaceutical enterprises have caused serious environmental pollution. The stereoscopic pollution effects on human health and the regional environment can't be ignored, especially in China who has high volume production in raw pharmaceutical material. Based on the angle of compound ecosystem, the ecological planning of the production and business operation in pharmaceutical enterprises, the promotion of clean production, and the establishment of ISO14000 environmental management system have become the key to solve these pollution problems brought by pharmaceutical enterprises. The clean production and environmental management system are complementary, namely relevant with at the same time different from each other. To promote the clean production in pharmaceutical enterprises, related hardware and soft ware system of the enterprise as well as the ecological design of its pharmaceuticals should be strengthened. Meanwhile, greater emphasis on the certification of ISO14000 environmental management system should be paid, along with hard work in the construction of management system and institutions in pharmaceutical industry.