The prosecution stage is one of the important stages of criminal proceedings that has a high impact on the later stages of criminal proceedings. different legal systems, by giving different discretionary powers to the authorities, try to filter the incoming cases and remove the crimes from the formal criminal process at the very early stages, thereby providing an opportunity for important crimes. The solutions that are foreseen for the exercise of this authority are the alternatives to prosecution. In the Iranian legal system, with the approval of the Criminal Procedure Code of 2013, alternatives to prosecution have been foreseen. In this article, using a descriptive-analytical method, we are trying to answer what are the challenges of the prosecution system in Iranian law and what are the solutions to overcome them and what is the efficient prosecution model. The results of the research indicate that the scope of alternatives to prosecution in the Iranian legal system is very limited and in cases where these alternatives have been foreseen, in practice it is not sufficient from the point of view of judgment, and these alternatives are not used. This has led to no assessment of the expediency of prosecution or not, and it is the same as the crimes at the prosecution stage, and no filtering occurs. In order to address these challenges, the scope of alternatives to prosecution should be expanded and the necessary training should be provided to officials.