The invention discloses an independent micro-grid layered coordinated control method based on different time scales. The method comprises the following steps of (1), according to the dynamic characteristics of voltage and frequency of an independent micro-grid system, dividing the fluctuation range of the voltage and frequency into three areas of A, B and C, wherein the area A represents that the deviation of the voltage and frequency is in a normal fluctuation range, the area B represents that the deviation of the voltage and frequency slightly exceeds the normal fluctuation range, and the area C represents that the deviation of the voltage and frequency seriously exceeds the normal fluctuation range; (2) monitoring and collecting the voltage U, the frequency f and the power P of the bus of the independent micro-grid, and determining the areas where the U and the f are located; (3) if the U and the f are located in the area A, keeping a storage battery energy storage system and a diesel generating set away from an adjustment process, if the U and the f are located in the area B, enabling the storage battery energy storage system in charge of primary control to participate in the adjustment process to achieve system power balance, and if the U and the f are located in the area C, enabling a secondary control diesel generator to participate in the adjustment process to achieve system power balance; (4) repeatedly collecting the U, the f and the P until the U and the f are determined to be located in the area A.