Currently, low Earth orbit (LEO) satellites are attracting great attention in the navigation enhancement field because of their stronger navigation signal and faster elevation variation than medium Earth orbit (MEO) satellites. To meet the need for real-time and precise positioning, navigation and timing (PNT) services, the first and most difficult task is correcting errors in the process of precise LEO orbit and clock offset determination as much as possible. Launched in 29 September 2018, the CentiSpace-1 (CS01) satellite is the first experimental satellite of LEO-based navigation enhancement system constellations developed by Beijing Future Navigation Technology Co. Ltd. To analyze the impact of the attitude model, carrier phase wind-up (PWU) and phase center variation (PCV) on precise LEO orbit and clock offset in an LEO-based navigation system that needs extremely high precision, we not only select the CS01 satellite as a testing spacecraft, but also the Gravity Recovery and Climate Experiment Follow-On (GRACE-FO). First, the dual-frequency global positioning system (GPS) data are collected and the data quality is assessed by analyzing the performance of tracking GPS satellites, multipath errors and signal to noise ratio (SNR) variation. The analysis results show that the data quality of GRACE-FO is slightly better than CS01. With residual analysis and overlapping comparison, a further orbit quality improvement is possible when we further correct the errors of the attitude model, PWU and PCV in this paper. The final three-dimensional (3D) root mean square (RMS) of the overlapping orbit for GRACE-FO and CS01 is 2.08 cm and 1.72 cm, respectively. Meanwhile, errors of the attitude model, PWU and PCV can be absorbed partly in the clock offset and these errors can generate one nonnegligible effect, which can reach 0.02~0.05 ns. The experiment results indicate that processing the errors of the attitude model, PWU and PCV carefully can improve the consistency of precise LEO orbit and clock offset and raise the performance of an LEO-based navigation enhancement system.