Since the establishment of the People’s Republic of China, investigation on duty crimes has undergone reforms and adjustments several times, supported by the amendments of relevant laws and regulations such as the criminal procedure law. What lies behind these reforms are the major changes in the political and judicial systems. Against the backdrop of the reform of the national supervision system, clarifying the relationship between investigation and supervision requires us to carefully sort out the pattern evolution of duty crime prosecution and to think over the effective connection of supervision and criminal proceedings in the perspective of criminal justice system. Our nation’s traditional investigation of duty crime has been featured with strong authoritarianism, which is in line with the amendment of our nation’s criminal procedure laws. What lies deeply behind the investigation is the game between punishing crimes and protecting human rights. Here are some examples: joint case handling against the background of anti-corruption campaigns before 1978, inquisitorial investigation dominated by procuratorial organs after 1979, and the combination of interrogative and adversarial modes of investigation based on the conception of human rights protection formed by the two revision of criminal procedure law since 1996. The evolution of duty crime prosecution modes is consistent with the maturity of due process, with a basic direction of rational expansion and legal regulation. It is directly reflected in the further advancement of the legislation of duty crime investigation, the regulation of power and the protection of rights. Under the background ofthe reform of the unified supervision system, the investigation of duty crimes has evolved into a new pattern, which is characterized by ″supervisory organs-led supervision, complemented by procuratorial organs investigation.″ The newly established supervision and investigation system is the continuation of the former duty crime investigation, which constitutes the basis for the effective connection between supervision and criminal proceedings from the perspective of criminal justice system. Through a careful study of the model evolution of duty crime prosecution in China, it is predicted that system construction and practice process of duty crime prosecution by supervisory organs will still be accompanied by reasonable expansion and effective regulation. That means the main value orientation of supervisory investigation will still be punishing crimes for a long time in the future, while human rights protection is an indispensable independent value in this process. The basis of supervision system reform based on effective supervision is aimed at the goal of reasonable regulation. In order to improve the system, it is necessary to clarify the application of the conceptions of human rights protection on the basis of respecting judicial laws and adhering to the conceptions of rule of law with the proportionality principle. By ″checking power with power″ and ″checking power with rights″, we can promote the transformation to rule of law of the criminal justice for duty crimes.