The currently employed algorithms for the magnetic field compensation of single-beam spin-exchange relaxation-free atomic magnetometers are excessively slow and unstable, which limits the use and commercialization of magnetometer arrays for biological magnetic measurement. This study proposes an improved trisection algorithm to compensate for the magnetic field around the vapor cell in an attempt to resolve these limitations. Through the constantly monitoring of the intensity of light emitted from a laser, the proposed algorithm reduces the time required to compensate for magnetic fields to 0.85 s in a single magnetometer, which is 9 times faster than the traditional algorithm, and to 26 s in a 36-channel magnetoencephalography equipment, which is 15.5 times faster than the traditional algorithm. In addition, an approximately 16% increase in measuring sensitivities is achieved based on the improved trisection algorithm compared with the traditional algorithm. These improvements can promote the usage efficiency and commercialization of biological magnetic measurement instruments. Furthermore, the improved trisection algorithm is verified using an experimental setup and the mathematical analysis and comparable experimental results demonstrate the effectiveness of the proposed algorithm.