This paper proposes an intelligent service optimization method based on a multi-agent collaborative evolution mechanism to address governance challenges in large-scale microservice architectures. These challenges include complex service dependencies, dynamic topology structures, and fluctuating workloads. The method models each service as an agent and introduces graph representation learning to construct a service dependency graph. This enables agents to perceive and embed structural changes within the system. Each agent learns its policy based on a Markov Decision Process. A centralized training and decentralized execution framework is used to integrate local autonomy with global coordination. To enhance overall system performance and adaptability, a game-driven policy optimization mechanism is designed. Through a selection-mutation process, agent strategy distributions are dynamically adjusted. This supports adaptive collaboration and behavioral evolution among services. Under this mechanism, the system can quickly respond and achieve stable policy convergence when facing scenarios such as sudden workload spikes, topology reconfigurations, or resource conflicts. To evaluate the effectiveness of the proposed method, experiments are conducted on a representative microservice simulation platform. Comparative analyses are performed against several advanced approaches, focusing on coordination efficiency, adaptability, and policy convergence performance. Experimental results show that the proposed method outperforms others in several key metrics. It significantly improves governance efficiency and operational stability in large-scale microservice systems. The method demonstrates strong practical value and engineering feasibility.