An error handling method, a memory storage device and a memory controlling circuit unit are provided. The method includes obtaining a finished event corresponding to a channel; determining whether the finished event is a failed event, if the finished event is the failed event; stopping an operation of the channel and performing a first update operation on a counting value corresponding to the channel; and if the finished event is not the failed event, keeping the counting value corresponding to the channel unchanged and processing the finished event. The step of the processing the finished event includes performing a second update operation on the counting value corresponding to the channel if the finished event is the failed event, and recovering the operation of the channel if the counting value matches a threshold criterion. Accordingly, it can improve the accessing performance.