Today’s society is a society of the knowledge economy, and the competition of enterprises is the competition of talents. The rapid development of science and technology and the fierce development of market competition have made the importance of performance management increasingly prominent in corporate management. The purpose of performance management is to explore and deal with some of the effects of various factors on employee performance and to tap the potential of employees, improve employee performance, and also bring a qualitative leap to the performance of the organization. The improvement of the employee performance management level has laid a solid foundation for the improvement of the organizational performance management level. However, there are still some difficulties in the implementation of performance management in my country at this stage, and the management effect is not obvious. Therefore, building a scientific, reasonable, and complete multiobjective optimization-based corporate performance optimization management decision-making and coordination mechanism is the primary task of today’s enterprises. This article will give a brief theoretical overview of the combination of system management theory and behavior management theory, MBO target management, and KPI indicators, build a multiobjective optimization model on an effective theoretical basis, and use genetic algorithms to obtain a weak Pareto effective solution that can optimize the enterprise with consideration of performance appraisal indicators. It also builds an agency model and an analysis of employee incentive plans, which clearly shows the relationship between the company and the management and employees, conducts a cross analysis of the needs of the company’s management and employees, and puts forward the best corporate performance considering the needs of employees; among them, the multiobjective optimization of corporate performance increased by 14% under the optimal management decision.