The natural ventilation systems of multi-story residential buildings are designed to meet the requirements for maximum air exchange. Their calculations under conditions significantly different from the standard, usually do not carry out and therefore do not provide measures to prevent their unstable operation. The article presents the results of the analysis of the ventilation system of a two-room section of a ten-story residential building using a mathematical model. To supply air to the apartment, ventilation valves are used. The air is removed from the apartments through two ventilation ducts. All apartments, except the last two floors, are connected to them via satellite channels. The system of equations of the model is based on the graph of the hydraulic network. It includes equations of the balance of air flow in the nodes of the graph and equations of pressure change in the links. In this case, the data presented in the catalogs of equipment manufacturers was used. The calculation results for conditions that differ from the design ones are presented, such as: significant differences in the supply air flow in individual apartments, the use of exhaust fans in some apartments, low outdoor temperature. The model under consideration allows us to explain the observed in practice air penetration through ventilation ducts from one apartment to another. It is shown that the main causes of this phenomenon are the low air transmission of modern window structures and the high hydraulic resistance of the supply valves, the use of ventilation ducts with various hydraulic resistances. The proposed approach allows already at the project stage to quantify the operation of the ventilation system in conditions that differ from standard and to optimize its design.