This paper presents a new method to improve the long-term frequency stability of an oven-controlled crystal oscillator (OCXO) without an external reference source. The frequency drift of the crystal oscillator can be obtained in real time by measuring the phase shift between the pins of the crystal resonator. In this paper, according to an equivalent circuit of a crystal oscillator, a linear equivalent mathematical model based on the phase shift of the crystal resonator and the output frequency is established. The experiments were conducted to observe the relation between the phase shift and frequency drift of the OCXO. At the same time, a crystal oscillator self-calibration frequency control system is established to improve the frequency drift of the OCXO. The results show that this method can effectively improve the drift of OCXOs. The OCXO drift rate was significantly improved from 1.53 10⁻¹⁰/day to 9.8 10⁻¹²/day, and after three days, it settled at 5.24 10⁻¹¹. The long-term frequency stability also underwent remarkable improvement, from 1.16 10⁻¹¹/1000 and 3.24 10⁻¹¹/10,000 to 3.47 10⁻¹²/1000 and 1.05 10⁻¹¹/10,000.