A method and system for adaptively finding reference voltages for reading data from a multi-level cell (MLC) flash memory is disclosed. According to one embodiment, a first total number of cells of the flash memory above a first threshold voltage in a shifted threshold voltage distribution is provided. Search to find a second threshold voltage such that a second total number of the cells above the second threshold voltage is approximate to the first total number. An initial reference voltage or voltages of the initial threshold voltage distribution are shifted with an amount approximate to a voltage difference between the second threshold voltage and the first threshold voltage, thereby resulting in a new reference voltage or voltages for reading the data from the MLC flash memory.