The invention discloses a method and a system for controlling the PH values of a methane tank. The method comprises the following steps of: detecting PH values of different areas in the methane tank by utilizing a plurality of PH sensors; comparing the PH values two by two, and judging whether a measuring differential value between any two PH values exceeds a preset PH differential value or not; and when the measuring differential value between any two PH values exceeds the preset PH differential value, generating a stirring signal and sending the stirring signal to a stirrer. Compared with the prior art, the method is operated without manual operation and is high in flexibility, and stirring are not performed according to regular time intervals and can be performed according to specific conditions in the methane tank, so that the PH values in the methane tank can be controlled better, and the condition of large temperature difference between different areas is avoided.