Due to the influence of the traditional viewpoint of “emphasizing the noumenon and neglecting the procedure” and the contradiction between punishing crime and protecting human rights， there still exists a lot of theoretical and practical problems in the supplementary investigation system in China， such as the illegibility of supplementary investigation right between public security organs and the procuratorial organs， long extension of supplementary investigation caused by unnecessary or over-due detainment. These problems are expected to be solved both in the sphere of legislation and judicial practice through further improving the supplementary investigation system， establishing the system of investigation under the procuratorial organ’s guide， strengthening the communication and cooperation mechanism between the public security and procuratorial organs， and authorizing the procuratorial organs rights of punishment.