A storage control system, and a method of operation thereof, including: a power-down module for powering off a memory sub-system; a decay estimation module, coupled to the power-down module, for estimating a power-off decay rate upon the memory sub-system powered up, the power-off decay rate is for indicating how much data in the memory sub-system has decayed while the memory sub-system has been powered down; and a recycle module, coupled to the decay estimation module, for recycling an erase block for data retention based on the power-off decay rate.