Entities mostly exist in heterogeneous forms in Internet of Things (IoT)， so solving heterogeneous issue is a vital task for developing IoT. On the basis of analysis on the characteristics of entities and their uploaded information in IoT， an agent-based heterogeneous entities relation service model was proposed. The functions of model include entity information data processing and entity service logic construction， and through using the new inter-objects dynamic relation calculation formula proposed in the paper，the heterogeneous data was transformed into their relation closeness（values），and the agent service sequence was generated based on it. Combining with the bipartite graph theory， the agent service logic was realized in IoT environment， which overcomes the heterogeneity that entities are unable to communicate with each other properly. In the model， entity interactions were completely replaced with agent interactions，and these agents were governed under the established service logic. Finally， the simulation experiment was performed on the model. And the result shows that not only can user's service requirements in IoT environment be met but also it is better than the traditional ontologies and semantics technology to deal with heterogeneous issues in the data updating， service quality and conflict handling.