Venture-capitalized commercial enterprises are an important part of economic development, and the comprehensive management model and innovation system of venture-capitalized commercial enterprises are studied to guide the benign development of the enterprises more scientifically. After defining the management model of venture capital class business enterprises, the factors affecting the optimization of business model are analyzed from the macro and micro perspectives, and analyzed specifically in the light of the actual situation. Based on the exploration of the comprehensive management model of the enterprise, the optimization is targeted. Guided by the value chain of the enterprise, the system innovation is realized by cultivating a perfect venture capital service system, forming a strategic alliance between enterprises, and establishing a cooperative investment management system internally. Through this research, it provides theoretical support for the real operation of enterprises.