With the rapid development of science and technology, big data technology is widely used in the field of criminal investigation, and synthetic investigation, predictive investigation and active investigation become the advantages of big data investigation. The use of personal information in big data investigation is increasing day by day, which intensifies the security and protection of citizens’ personal information. At present, protection of citizens’ personal information in big data investigation faced with the following difficulties: the expansion of the subject of infringement, the universality of the object of infringement, the secrecy of the way of infringement, and the severity of the harmful consequences. The reasons are the lack of legal regulation, the limitation of internal prevention and control, the convenience of access channels, and the increase of leakage risk. Identification is necessary to strengthen the constitutional legal regulation, perfect the internal prevention and control mechanism, construct the pre-examination mechanism and establish the relief guarantee mechanism in the investigation of the inherent aggression of big data to citizens’ personal information.