A method of active Flash management is provided. The method is applied to a controller of a memory device, where the controller is utilized for accessing a Flash memory in the memory device, and the Flash memory includes a plurality of blocks. The method includes: extracting high level information of a file system of the Flash memory from contents stored in the Flash memory; and according to the high level information, managing operations that the controller performs on the Flash memory, in order to optimize at least one portion of the operations. An associated memory device and the controller thereof are further provided.