A hybrid storage apparatus including a non-volatile memory module, a hard disk module, and a hybrid storage medium controller is provided. The hybrid storage medium controller groups physical blocks of the non-volatile memory module into at least a storage area and a replacement area, and the hybrid storage medium controller configures a plurality of logical blocks for mapping to the physical blocks in the storage area and configures a plurality of logical disk addresses for mapping to physical disk addresses of the hard disk module. The hybrid storage medium controller further configures a plurality of logical access addresses to be accessed by a host system and initially maps a portion of the logical access addresses to the logical blocks and the other logical access addresses to a portion of the logical disk addresses. Accordingly, the hybrid storage apparatus can have improved data access performance and prolonged lifespan.