One embodiment provides a system and method for facilitating error-correction protection in a storage device. In response to a write request, the system organizes a block of data in a two-dimensional (2D) array, forms a plurality of first-dimension sub-blocks by dividing the 2D array along a first dimension, and forms a plurality of second-dimension sub-blocks by dividing the 2D array along a second dimension. In response to determining that second-dimension error correction code (ECC) encoding is enabled, the system performs second-dimension ECC encoding on the second-dimension sub-blocks to generate a set of second-dimension ECC bits and performs first-dimension ECC encoding on the first-dimension sub-blocks and the second-dimension ECC bits to generate a set of first-dimension ECC bits. The system writes the data block along with the second-dimension ECC bits and the first-dimension ECC bits to the storage device. The data block and the second-dimension ECC bits are mapped to separate physical addresses in the storage device.