A memory system may include: a memory device including a plurality of dies; and a controller suitable for controlling the memory device, wherein the controller includes: a buffer including a plurality of entries suitable for temporarily storing target data; a monitor suitable for comparing a size of the target data with a predetermined threshold value; a buffer manager suitable for determining, when the size of the target data is equal to or greater than the predetermined threshold value, a skip value based on physical information of the memory device, and storing a start entry and an end entry in which the target data is stored; and a processor suitable for controlling the memory device to perform a program operation on the target data through an interleaving programming method based on the start entry, the end entry, and the skip value.