A data management method, a memory controller and an embedded memory storage apparatus are provided. The embedded memory storage apparatus has a plurality of physical blocks and each of the physical blocks has fast physical pages and slow physical pages. The method includes detecting a status of a state indication unit. The method further includes automatically reading data stored in the embedded memory storage apparatus, using the fast and slow physical pages of the embedded memory storage apparatus to re-store the data and marking status of the state indication unit as a second status when the status of the state indication unit is a first status. Accordingly, the storage space of the embedded memory storage apparatus can be efficiently used.