A pendulous integrating gyro accelerometer is installed in the inertial navigation system as a single-axis sensitive accelerometer. It is generally used to sensitive apparent acceleration in the direction of the input axis. Meanwhile, it will be subjected to transverse acceleration, which is perpendicular to the direction of the input axis. The PIGA is subjected to transverse acceleration, which generates a large amplitude of the float cyclic swing around the input axis, thus affecting the accuracy of the instrument. To address this problem, the force analysis of the float is carried out, and the dynamic equations of radial motion of the float have been established under the simultaneous action of transverse acceleration and sensitive acceleration. A proportional-integral control method of magnetic suspension is proposed on the basis of the purely proportional control method. The new method can provide a greater stiffness for the magnetic suspension system to overcome pendulous moments and eliminate the static position error. It would suppress the amplitude of the float swing. A Simulink simulation and comparison are conducted on the radial motion of the float under two control methods. When the transverse acceleration 0.866g and the sensitive acceleration 0.5g act simultaneously, the amplitude of the float swing decreases from ±0.62 μm to ±0.24 μm. When the transverse acceleration 3g and the sensitive acceleration 1g act simultaneously, the amplitude of the float swing decreases from ±2.2 μm to ±0.74 μm. By carrying out centrifuge tests on PIGA, it is found that the amplitude of the float swing decreased from ±2 μm to ±0.5 μm at a transverse acceleration 3.15g and a sensitive acceleration 0.313g. When the transverse acceleration and the sensitive acceleration change at the same time, the amplitude of the float swing is decreased by about 50%. The results show that the proportional-integral control method of magnetic suspension can significantly suppress the amplitude of the float swing and really reduce the swing amplitude by 50% or more compared with the pure proportional control method of magnetic suspension. The new method has practical engineering significance and can improve the instrumentation measurement accuracy when PIGA is subjected to lateral acceleration in use.