The recently developed magic-intensity trapping technique of neutral atoms efficiently mitigates the detrimental effect of light shifts on atomic qubits and substantially enhances the coherence time. This technique relies on applying a bias magnetic field precisely parallel to the wave vector of a circularly polarized trapping laser field. However, due to the presence of the vector light shift experienced by the trapped atoms, it is challenging to precisely define a parallel magnetic field, especially at a low bias magnetic field strength, for the magic-intensity trapping of 85Rb qubits. In this work, we present a method to calibrate the angle between the bias magnetic field and the trapping laser field with the compensating magnetic fields in the other two directions orthogonal to the bias magnetic field direction. Experimentally, with a constant-depth trap and a fixed bias magnetic field, we measure the respective resonant frequencies of the atomic qubits in a linearly polarized trap and a circularly polarized one via the conventional microwave Rabi spectra with different compensating magnetic fields and obtain the corresponding total magnetic fields via the respective resonant frequencies using the Breit–Rabi formula. With known total magnetic fields, the angle is a function of the other two compensating magnetic fields. Finally, the projection value of the angle on either of the directions orthogonal to the bias magnetic field direction can be reduced to 0(4)° by applying specific compensating magnetic fields. The measurement error is mainly attributed to the fluctuation of atomic temperature. Moreover, it also demonstrates that, even for a small angle, the effect is strong enough to cause large decoherence of Rabi oscillation in a magic-intensity trap. Although the compensation method demonstrated here is explored for the magic-intensity trapping technique, it can be applied to a variety of similar precision measurements with trapped neutral atoms.