Abstract: Objective To understand the national reporting level of notifiable communicable diseases in hospitals included in national notifiable communicable disease surveillance system, the sampling method and protocol were designed. Methods Based on data from the previous studies on the reporting rates of communicable diseases since 2005 and the data from national notifiable communicable disease surveillance system, the sampling protocol was designed according to the theory and methods of multistage stratified cluster sampling and the overall sample size, sample size of each stratum, sample points at each stage were calculated. Results The total sample size was 1998. All the samples were in four strata: provincial hospitals (n=270), prefecture hospitals (n=540), county hospitals (n=864), and township hospitals (n=324). According to the design of the study, the hospitals were randomly selected from 54 townships in 27 counties in 27 prefectures in 9 provinces. Conclusion It was the first time for us to use multistage stratified cluster sampling method to conduct communicable disease reporting rate assessments. To avoid sampling error, a higher degree of confidence was set to ensure the accuracy and reliability of sampling inference. Thus, the manpower, resources and investigation time were reduced and the efficiency of investigation was improved.