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Innovation and institutional governance are the key enabling factors of cluster ecosystem development. Its synergistic effects play an important role in enhancing ecosystem competitiveness. In this paper, pseudocode language is applied to cluster ecosystem cooperative model reasoning. The coordination and optimization of the innovation system and institutional governance system were studied in a biomedical cluster. Besides, Pearson algorithm was used to test the correlation degree of elements in three Chinese biomedical clusters. The results show that, in Zhangjiang and Nanchang biomedical clusters, the synergistic correlation coefficient between the innovation system and the institutional governance system fluctuates around 0.8. However, in Tonghua biomedical cluster, the synergy correlation coefficient fluctuated around -0.2. The fluctuation range between the two clusters was large. After adjusting the range of order parameters, the rank of synergy trend was Zhangjiang > Nanchang > Tonghua. Finally, further analysis shows that Zhangjiang and Nanchang biomedical clusters can achieve the optimal synergy state by adjusting innovation and institutional governance, but Tonghua cannot. Therefore, the collaboration between the innovation system and institutional governance system provides some reference for the high-quality development of the cluster ecosystem. [ABSTRACT FROM AUTHOR]