An encoding control method, a memory storage device and a memory control circuit unit are provided. The method includes: reading a plurality of first data units by a plurality of first host to device (H2D) access operations; generating at least one first parity unit according to the first data units; transmitting the first parity unit to the host system by at least one first device to host (D2H) access operation; reading a plurality of second data units by a plurality of second H2D access operations; generating at least one second parity unit according to the first parity unit and the second data units without reading the first parity unit from the host system; transmitting the second parity unit to the host system by at least one second D2H access operation; and storing the first data units and the second data units to a first physical unit.