A method and a system for programming a multi-level cell (MLC) memory are provided. A first count is 1 initially. The method comprises the following steps. A first energy is set. The first energy is applied to alter a resistance of a cell of the MLC memory. The first count is increased by 1 after performing the step of applying the first energy. In the step of setting the first energy, the first energy is a ⁢ ⁢ first ⁢ ⁢ initial ⁢ ⁢ energy a ⁢ ⁢ predetermined ⁢ ⁢ value initially and the first energy is changed by increasing or decreasing the ⁢ ⁢ first ⁢ ⁢ initial ⁢ ⁢ energy the ⁢ ⁢ predetermined ⁢ ⁢ value the ⁢ ⁢ first ⁢ ⁢ count .