In order to solve the limitation of traditional time interval measurement method which is limited by clock resolution and high hardware cost, a dual-frequency time interval measurement method is proposed. In this method, phase perturbation or equivalent phase perturbation is performed on the received clock signal at the receiver, so that the received clock signal has a definite phase probability distribution in one period of the signal to be measured. Then, through multiple sampling and statistical calculation, the reading error caused by low clock resolution is eliminated. The simulation and experimental results show that the measurement error of the dual-frequency time interval measurement method is 0.06 ns, which reaches the measurement accuracy of sub-nanosecond and breaks the limit of clock resolution.