Transplanting is a core part of factory nurseries and is a key factor in determining the healthy growth of seedlings. While transplanting has a single operational function, the complete process of sorting, transplanting and replanting is complex. This paper innovatively proposes an intelligent multi-functional seedling transplanting system, where the sorting, transplanting and replanting functions can be achieved with a single machine. This paper proposes the key strategies of seedling dynamic detection during transplanting and performing transplanting and replanting within the same tray, thus realizing the integration and miniaturization of the all-in-one machine. Then, through the flat design of the transplanting–replanting mechanism and the construction of a multi-module cooperative control strategy, a stable and reliable multi-functional synchronous operation is realized. Finally, the integrated operation experiment shows that the transplanting efficiency of the whole machine is 5000 plants/h, and the qualification rate after replanting is as high as 99.33%, which meets the operational needs of factory nurseries.