A flash memory storage device, a controller thereof, and a data programming method are provided. The flash memory storage device has a flash memory comprising a plurality of physical blocks, each physical block includes a plurality of physical addresses, and the physical addresses comprises at least one fast physical address and at least one slow physical address. The method comprises at least grouping the physical blocks into a data area and a spare area; setting a predetermined block number; obtaining m physical blocks from the spare area, receiving a write command comprising a write data and a logical address, determining a logical address range of a buffer according to the logical address and the predetermined block number. When all logical addresses to be programmed with the write data are within the logical address range of the buffer, using a fast mode to program the data into the m physical blocks.