Period estimation of X-ray pulsars plays an important role in X-ray pulsar based navigation (XPNAV). The fast Lomb periodogram is suitable for period estimation of X-ray pulsars, but its performance in terms of frequency resolution is limited by data length and observation time. Longer observation time or oversampling can be employed to improve frequency analysis results, but with greatly increased computational complexity and large amounts of sampling data. This greatly restricts real-time autonomous navigation based on X-ray pulsars. To resolve this issue, a new method based on frequency subdivision and the continuous Lomb periodogram (CLP) is proposed to improve precision of period estimation using short-time observation data. In the proposed method, an initial frequency is first calculated using fast Lomb periodogram. Then frequency subdivision is performed near the initial frequency to obtain frequencies with higher precision. Finally, a refined period is achieved by calculating the CLP in the obtained frequencies. Real data experiments show that when observation time is shorter than 135 s, the proposed method improves period estimation precision by 1–3 orders of magnitude compared with the fast Lomb periodogram and fast Fourier transform (FFT) methods, with only a slight increase in computational complexity. Furthermore, the proposed method performs better than efsearch (a period estimation method of HEAsoft) with lower computational complexity. The proposed method is suitable for estimating periods of X-ray pulsars and obtaining the rotation period of variable stars and other celestial bodies.