The article presents a methodology for optimizing transport costs with the use of modeling in PTV Visum software package. Based on the analysis of transport problems in large urban agglomerations, a quality criterion was chosen for the assessment of passenger transport performance. An approach has been proposed to introduce transport hub systems with the purpose to minimize time spending on transfer, in particular, and on trip by public transport in a whole. This optimization method for transport spending represents an algorithm of 3 key blocks: the formation of transport model for being studied agglomeration, the placement conditions and the choice of transport hub locations. The model is formed on the base of 4-step approach, the trips distribution in a network is based on entropy approach which is considered in the second section in more details. The placement conditions go from an idea to minimize time total spending on moving, the number of hubs being introduced is limited by their construction financing. The approach application is demonstrated on the example of northwestern urban agglomeration Sertolovo-Osinovaya Roshcha-Pargolovo which represents being actively built-up residential districts on St. Petersburg city border. The specificities of its transport network, including also hubs and highways with complicated traffic, are determined. Based on open sources and statistical data, a transport model was developed, its calibration was pursued. 3 options for placing transport hubs on network of the agglomeration are presented. As a result of the research, the analysis for the options of transport hub placements is presented and the most promising option from the view of purpose meaning achievement for hub placement in being considered agglomeration is proposed.