A ventilation system usually runs on a certain schedule. The boundary conditions, such as the time-dependent outdoor particle concentrations and indoor particle generating sources, vary dynamically. Ventilated rooms are connected to ventilation ducts and filters, and indoor particle concentration and particle deposition on duct surfaces are interdependent. Thus it is important to study particle transport in the entire ventilation system and take the dynamic characteristics into account to assess particle pollution in the entire system more accurately. A generalized model is proposed in this study to estimate particle concentration throughout an entire ventilation system as well as mass loading of particles on ventilation components. Model equations describe particle movement in different ventilation components, including filters, ducts, and rooms. Penetration factors are adopted for filters and ducts, and particle concentrations in rooms are calculated by a lumped parameter method. This generalized model can be applied to any ventilation system, and a new software, PROBE-PM, was developed based on the presented model. Four case studies are carried out using this new software to demonstrate the application of the model.