The criminal justice identification system in trial is an inseparable system, but Chinese scholars’ empirical research on criminal justice identification system is generally based on a single link, selecting a certain court or a few cases in last year or in recent years for field research. Based on the data of 600 judgment documents before and after the second revision of the Criminal Procedure Law, this article observes the operation of Chinese criminal justice identification system in large-scale and long-term trials. It is found that the criminal justice identification system has the characteristics of low objection rate, low application rate and high acceptance rate in the trial operation. After the second revision of the Criminal Procedure Law, the operation of the criminal justice identification system has not substantially improved. In the investigation and prosecution stage, the maximum dispute is resolved before the trial. In the trial, defense ability of the defender and the ability of the judge to examine evidence should be taken into consideration, so as to maximize the efficiency of the lawsuit and rationally allocate judicial resources, and to find out the disputed facts of the case through appraisal substantial operation in the trial.