The eLoran system is an international standardized positioning, navigation, and timing service system, which can complement global navigation satellite systems to cope with navigation and timing warfare. The eLoran receiver measures time-of-arrival (TOA) through cycle identification, which is key in determining timing and positioning accuracy. However, noise and skywave interference can cause cycle identification errors, resulting in TOA-measurement errors that are integral multiples of 10 μs. Therefore, this article proposes a cycle identification method in the joint time–frequency domain. Based on the spectrum-division method to determine the cycle identification range, the time–domain peak-to-peak ratio and waveform matching are used for accurate cycle identification. The performance of the method is analyzed via simulation. When the signal-to-noise ratio (SNR) ≥ 0 dB and skywave-to-groundwave ratio (SGR) ≤ 23 dB, the success rate of cycle identification is 100%; when SNR ≥ ？13 dB and SGR ≤ 23 dB, the success rate exceeds 75%. To verify its practicability, the method was implemented in the eLoran receiver and tested at three test sites within 1000 km using actual signals emitted by an eLoran system. The results show that the method has a high identification probability and can be used in modern eLoran receivers to improve TOA-measurement accuracy.