After the interruption of the timing service, the increase in clock offset is a critical issue for the global navigation satellite system (GNSS)-disciplined oven-controlled crystal oscillator (OCXO). Current timekeeping methods for GNSS-disciplined OCXO have some drawbacks, such as high computational complexity, inadequate consideration of temperature effects, and insufficient separation of the impacts of temperature and aging. To address this issue, this study proposes a timekeeping method using a dual iterative algorithm. First, the external iteration separates the clock offset caused by temperature and aging. Then, the internal Gauss–Seidel iterative algorithm estimates the temperature and aging coefficients. During the timing service interruption phase, the model estimates and compensates for the frequency offset in real time using the coefficients. The proposed method demonstrates improved performance compared with OCXO in the free state and compensated by a second-order polynomial model, with better accuracy, drift rate, and long-term stability. The time offset is better than 4 μs over 24 h, representing an improvement of over 95% compared with the OCXO in the free state.