This study focuses on management ways within a city multi-floor manufacturing cluster (MFMC). The application of MFMC in megapolises is closely related to the problem of urban spatial development and the problem of matching transport and logistics services. The operation of the MFMC depends on the efficiency of production and transport management considering technical, economic, end environmental factors. Therefore, conditions affecting decision-making in the field of production planning by MFMCs and accompanying transports within the agglomeration area with the use of the production-service platform were presented. Assumptions were created for the decision model, allowing for the selection of partners within the MFMC to execute the production order. A simplified decision model using the Hungarian algorithm was proposed, which was verified with the use of test data. The model is universal for material flow analysis and is an assessments basis for smart sustainable supply chain decision-making and planning. Despite the narrowing of the scope of the analysis and the simplifications applied, the presented model using the Hungarian algorithm demonstrated its potential to solve the problem of partner selection for the execution of the contract by MFMC.