Background Countries in the world have taken actions to prevent venous thromboembolism (VTE) in hospitals. We have conducted a study in China to assess the establishment of hospital-based systems for VTE prevention and management. Methods A nationwide hospital survey was conducted in China to collect hospital-level metrics on their system for VTE prevention between 2019 and 2020. We analyzed hospital-level metrics potentially influencing the implementation of thromboprophylaxis using a multivariable regression model. Characteristics of the hospital, organizational structure, quality control, and staff training were analyzed. Results Among 435 hospitals responding to the survey, 328 (75.4%) were able to implement thromboprophylaxis. They performed VTE and bleeding risk assessments and had prophylactic interventions. Institutional VTE steering committee and unit-based working group were set up in 317 (72.9%) and 339 (77.9%) hospitals, respectively. More than 80% of the hospitals performed quality control and staff training. In contrast, digitalization of risk assessment was only accomplished in 196 (45.1%) hospitals. Proportions of the aforementioned metrics were consistently higher in tertiary hospitals than secondary hospitals (P < 0.01) except for quality control. There were geographical disparities in the establishment of VTE steering committees (P = 0.0004). In multivariable analysis, VTE steering committee was an independent factor for the implementation of thromboprophylaxis (odds ratio, 2.22, 95% confidence interval, 1.17-4.23). Working group, quality control, and training on VTE were also positively associated with the implementation of thromboprophylaxis. Conclusions In-hospital VTE prevention has been undertaken in China, but system establishment remains suboptimal. Implementation of VTE prevention programs was associated with a decrease in thrombolytic events. Hospitals with VTE steering committees performed better on implementing preventive strategies. Suboptimal adoption of information digitization was identified, and the implementation of computer supporting techniques would be expected to improve the implementation of thromoboprophylaxis.