A spherical joint is a commonly used mechanical hinge with the advantages of compact structure and good flexibility, and it becomes a key component in many types of equipment, such as parallel mechanisms, industrial robots, and automobiles. Real-time detection of a precision spherical joint clearance is of great significance in analyzing the motion errors of mechanical systems and improving the transmission accuracy. This paper presents a novel method for the micro-clearance measurement with a spherical differential capacitive sensor (SDCS). First, the structure and layout of the spherical capacitive plates were designed according to the measuring principle of capacitive sensors with spacing variation. Then, the mathematical model for the spatial eccentric displacements of the ball and the differential capacitance was established. In addition, equipotential guard rings were used to attenuate the fringe effect on the measurement accuracy. Finally, a simulation with Ansoft Maxwell software was carried out to calculate the capacitance values of the spherical capacitors at different eccentric displacements. Simulation results indicated that the proposed method based on SDCS was feasible and effective for the micro-clearance measurement of the precision spherical joints with small eccentricity.