Objective To discuss medical staff's salary level and its satisfaction degree of Public Hospitals in Nanjing to provide scientific basis for salary system reform. Methods A total of 965 staffs from public hospitals in Nanjing were investigated by questionnaire survey. Their salary level and its satisfaction degree was analyzed by descriptive analysis, Kruskal-Wallis test, t-test, ANOVA, and multivariate linear regression analysis. Results The annual income of medical staff is RMB 88 600 per person with post difference and hospital grade difference; The expected annual average income of employees is about 2 times of the current average annual salary, and 2 or 3 times of the average social wage; The overall salary level satisfaction score was 3.06 which was at general level; The score of all dimensions in turn is external equity, individual fairness and internal fairness; Through multivariate linear regression analysis, the overall satisfaction had significantly difference among age, technical class, positions and hospital grade. Conclusion The salary system reform in public hospitals should strive to improve the salary level, widen the income gap between different posts reasonably, and pay attention to the non-economic compensation, in order to effectively promote the health and sustainable development of public hospitals.