A method of operating a multi-level cell is provided. The method includes the following the steps. (a) The multi-level cell is operated until a threshold voltage is larger than a pre-programming threshold voltage. And (b) the multi-level cell is operated until the threshold voltage is larger than a target programming threshold voltage and smaller than the pre-programming threshold voltage. Moreover, between the step (a) and the step (b), further comprises (c) A first verification step is performed. If the threshold voltage is smaller than the pre-programming threshold voltage, then repeat the step (a). Furthermore, after the step (b), further comprises (d) a second verification step is performed. If the threshold voltage is larger than the pre-programming threshold voltage, repeat the step (b), and if the threshold voltage is smaller than the target programming threshold voltage, repeat the steps (a)-(d).