The invention relates to a method and system used for Flash balance storage. The method includes the following steps that first, whether an erase flag exists or not in a current sector in which writing will be performed is checked, and if not, the current sector is formatted, and a flag is set; second, whether data are written in the current sector for the first time or not is checked, if yes, a next sector of the current sector is formatted firstly, the ERASE_FLAG is set, and then a USED_FLAG is written into the sector; third, whether the remaining space of the current sector is enough for writing a current data package or not is judged, and if the space is enough, the data are written into the current position, and the current operating address g_SectorInfo.cur_addr is updated; if the space is not enough, the operation skips into the next sector; fourth, whether the written-in data can pass verification or not is checked, and if not, the operation skips into the next sector, and the first step is executed.