This paper takes the merging unit as point cut of smart substation secondary system data source and analyzes the problems of present sampling system. A high reliability sampling way is proposed, based on which a new type of merging unit is designed. The new merging unit owns abnormal sampling data analysis and processing function. It can quickly and accurately distinguish the abnormal data, send information to the relay protection in the substation and help the relay protection to avoid incorrect action. The research can highly improve the reliability of the sampling in the smart substation with analysis and verification.