A method and system for estimating open circuit voltage of lithium ion batteries with temperature input, that has the following steps: step 1 the undetermined equation for estimating open circuit voltage with temperature input is derived according to the gas-liquid dynamic model; step 2: the estimation equation parameters are identified according to the experimental data and put into the undetermined equation for estimating open circuit voltage in the step 1 to obtain a complete equation for estimating open circuit voltage; step 3: the method for estimating open circuit voltage with temperature input is designed according to the complete equation for estimating open circuit voltage.