A data writing method for a re-writable non-volatile memory module and a memory controller and a memory storage apparatus using the same are provided, wherein the re-writable non-volatile memory module has a plurality of physical writing units, and each of the physical writing units has a plurality of physical writing segments. The data writing method includes identifying at least one non-used segment among the physical writing segments of each of the physical writing units and writing a plurality of segment data streams into the physical writing units, wherein the non-used segments of the physical writing units are not used for writing the segment data. Accordingly, the data writing method can effectively use normal physical writing segments in the physical writing units.