The invention discloses a temperature control method and system of a marsh gas tank. The method comprises the following steps: using multiple temperature sensors to detect temperature values of different regions in the marsh gas tank; performing pairwise comparison on the temperature values, and judging whether the measurement difference between any two temperature values exceeds a preset temperature difference; and when the measurement difference between any two temperature values exceeds the preset temperature difference, generating a stirring signal, and sending to a stirrer. Compared with the prior art, the method avoids manual operation, stirring is not performed at fixed time intervals, and stirring can be performed according to specific situations in the marsh gas tank, thereby achieving higher flexibility. Besides, the invention can realize better control on the temperature in the marsh gas tank, and avoids the situation that a big temperature difference exists among different regions.