A memory system, a memory controller and an operating method are disclosed. By determining, based on status check delay information, a time point at which a status check command is sent to a memory device and updating the status check delay information while the memory device is in an idle state, it is possible to minimize a degradation in the performance of a program operation for the memory device including a plurality of memory dies, and it is possible to reflect a variation in an operation characteristic of the memory device, on the program operation.