The purpose of this study was to construct the model of organization system, management, training and surveillance in healthcare-associated infection prevention and control (IC) of primary health care institutions and identify its effect on patient safety and decreasing economic burden by standardizing IC. A cross-sectional survey was conducted with questionnaires. Data were collected from 268 primary health care institutions in Hubei province, China. Hypotheses on the model of IC were analyzed by means of confirmatory factor analysis and structural equation modeling. The results showed that the fit indices of the hypothesized model of IC satisfied recommended levels: root mean square error of approximation (RMSEA)=0.071; comparative fit index (CFI)=0.965; tucker-lewis index (TLI)=0.956; weighted root mean square residual (WRMR)=1.014. The model showed that organization system had a direct effect on management (=0.311, P<0.01), and training (=0.365, P<0.01). Management and training played an intermediary role that partially promoted organization system impact on surveillance. Results also showed that institutional factors such as the number of physicians, the number of nurses, the designated capacity of beds, the actual number of open beds and surgery trips had positive impacts on management (=0.050, P<0.01; =0.181, P<0.01; =0.111, P<0.01; =0.064, P<0.01; =0.084, P=0.04) and training (=0.21, P=0.03; =0.050, P=0.02; =0.586, P=0.01; =-0.995, P=0.02; =-0.223, P=0.03). In conclusion, the model of organization system, management, training and surveillance in IC of primary health care institutions is valuable for guiding IC practice.