State of health diagnosis and estimation of lithium-ion batteries is a key feature of an advanced battery management system. Electrochemical impedance spectroscopy is frequently used for the state of health diagnosis and estimation. In the paper, the charge transfer resistance of the battery is obtained by fitting the impedance spectroscopy with an equivalent impedance model to estimate state of health. And an analytical calculation model with temperature and state of charge as inputs is derived and verified considering their effect on the charge transfer resistance. With the calculation model, the charge transfer resistance at randomly selected state of charge and temperature is converted to the standard state to be comparable for the state of health estimation. It is indicated that state of health estimated with the converted and the direct fitted charge transfer resistance agree well. The battery state of health estimation method with the converted charge transfer resistance eliminates the need to specifically control the temperature and state of charge during the impedance spectrum measurement. It benefits the practical application of the state of health estimation with electrochemical impedance spectroscopy.