Based on Josephson junction (JJ), superconducting quantum bit (qubit) is operated at frequencies of several GHz. Dissipation of JJs in this frequency range can cause energy relaxation in qubits, and limit coherence time, therefore it is highly concerned and needs to be determined quantitatively. The dissipation of JJs can be quantified by microwave quality factor. It is usually done at very low temperature (~mK) to determine whether a JJ is suitable for qubit devices by measuring the quality factor. In this paper, a method based on nonlinear frequency response of JJs is proposed to determine the quality factor. This method can be used in thermal activation regime, which may bring great conveniences to experiments. To analyze high frequency properties of JJs, the dynamic equation of a current-biased JJ, which describes high frequency oscillation of the JJ, is introduced. A fourth-order potential approximation is used to obtain the analytical equation of non-linear response. The dependence on quality factor, as well as on amplitude, of difference between JJ’s plasma frequency and resonant frequency, is derived from the equation. The approximate treatment is quantitatively validated by our numerical simulations with practical JJ parameters including different environment influences. Thus, based on nonlinear frequency response of JJs, a reliable and simple method to determine quality factor of JJ is proposed, which is desirable for exploring JJ based microwave devices such as parametric amplifier, superconducting qubit. Being driven well into the nonlinear microwave response regime, due to frequency-amplitude interaction, the resonant frequency of a current bias JJ deviates from the JJ’s plasma frequency. The deviation is directly related to the microwave quality factor. Hence, the quality factor can be deducted from the experimental measurement of the resonant frequency deviation, with different microwave power values applied. In comparison with linear resonance experiment, the nonlinear resonance used by the proposed method produces stronger signal. Therefore it is more robust against external noise. When being conducted at high temperature, the proposed method is more reliable. The accuracy of the measured quality factor primarily depends on those of the JJ’s parameters such as critical current and capacitance, while those parameters can be experimentally determined with high precision.