Effective institution supply is critical to the successful promotion of China’s current Supply-Side Reform and Economic Transformation and Upgrading. Based on the fact that a deviation exists between node enterprises’ perception of institutions’ effectiveness and significance, the paper constructs a moderated mediation model about institution-based trust’s effects on node enterprises’ aspiration to repeat cooperation from the perspective of collaboration trust in the supply chain. By a sample of 548 supply chain node enterprises’ survey, the moderated mediation model is proved: (1)Node enterprises’ institutional trust not only has a significant, direct positive influence but also has a significant, indirect positive effect on their aspiration to repeat cooperation through their collaboration trust in the supply chain (a partial mediator). (2)The deviation between node enterprises’ perception of institutions’ efficiency and significance moderates the mediating effect of collaboration trust significantly. In detail, collaboration trust’s mediating effect will be more strongly weakened as the deviating degree increases. The results not only enrich Chinese contextualization research on institutional trust, but also put forward operationalized paths to ensure effective and sufficient institutions during China’s current Supply-Side Reform and Economic Transformation and Upgrading.