At present, the ceiling cassette fan-coil unit (CCFU) is widely used in Chinese hospitals. However, enough attention has not been paid on filter installation in CCFU. This will cause secondary pollution inside the CCFU, which may increase the risk of nosocomial infection. With the increasingly serious condition of atmospheric pollution and the complexity for coexistence of bacteria and virus in hospital, it is urgent for owners and operators of hospital to select suitable filters for CCFU. In this study, three kinds of air filters (G4, M5 and F7) were installed in a consulting room, respectively. Indoor air was re-circulated by CCFU. The performance of air filter was evaluated by monitoring the decay rate of particle concentration within a period corresponding to the average regular consulting time. It is found that the overall particle removal efficiency (via filter-integrated CCFU) (OPRE) increases with the increase of filter's classification level. Upgrading the G4 filter to M5 or F7 filter can significantly reduce indoor particle concentration. Compared with F7 filter, the performance improvement of the M5 filter is mainly obtained for particles with diameter 0.85–3.5 μm. As far as the dynamic variation of particle concentration in the period studied is concerned, there is an exponential relationship between OPRE and clean air delivery rate (CADR). Since the concentration of bacteria is correlated to that of particles with diameter close to 3 μm, it is suggested to install M5 filter for this application, which provided the basis for selection of filter in CCFU for hospitals.