To enhance the accuracy of micro-Newton thrust measurements via a torsion pendulum, addressing microgravity coupling effects caused by platform tilt and pendulum mass eccentricity is crucial. This study focuses on analyzing and minimizing these effects by alleviating reference surface tilt and calibrating the center of mass during thrust measurements. The study introduced analysis techniques and compensation measures. It first examined the impact of reference tilt and center of mass eccentricity on the stiffness and compliance of the torsion pendulum by reconstructing its dynamic model. Simscape Multibody was initially employed for numerical analysis to assess the dynamic coupling effects of the tilted pendulum. The results showed the influence of reference tilt on the stiffness and compliance of the torsion pendulum through simulation. An inverted pendulum was developed to amplify the platform’s tilt angle for microgravity drag-free control. Center of mass calibration can identify the gravity coupling caused by the center of mass position. Based on the displacement signal from the capacitive sensor located at the end of the inverted pendulum, which represents the platform’s tilt angle, the pendulum’s vibration at 0.1 mHz was reduced from 5.7 μm/Hz1/2 to 0.28 μm/Hz1/2 by adjusting the voltage of piezoelectric actuator. Finally, a new two-stage torsion pendulum structure was proposed to decouple the tilt coupling buried in both pitch and roll angle. The study utilized theoretical models, numerical analysis, and experimental testing to validate the analysis methods and compensation measures for microgravity coupling effects in torsion pendulums. This led to a reduction in low-frequency noise caused by ground vibrations and thermal strains, ultimately improving the micro-Newton thrust measurement accuracy of the torsion pendulum through the platform’s drag-free control.