The vaccination system is divided into two categories in China. The first is mandatory vaccination, mostly free and using domestic vaccines under the National Immunization Program. The second is alternative vaccination, which patents must pay for. In March 2016 Shandong Province in China, a vaccine scandal occurred, which is known as the Shandong problematic vaccines incident. The incident involved 24 provinces and regions in China, The vaccine safety affects hundreds of millions of people. And all the problematic vaccines involved are second category vaccines. It exposed a variety of existing problems for the Chinese second category vaccines supervision system. Based on the analysis perspective of supervision elements, this paper makes a case study by analyzing the five supervision elements, which include: the subject and objects of supervision, supervision institutions, supervision resources and supervision environment. And it focuses on the problems of the Chinese second category vaccines supervision system exposed in the case, including: the administration level and the team scale of supervision subject-as not match with its duty; the interestoriented awareness of supervision objects being insufficient; the vaccine tracking institution not being complete; the professional supervision of human resources being insufficient; the participation of social supervision being insufficient.