This paper presents a novel method for estimating the temperature of magnetic nanoparticles (MNPs) based on AC magnetization harmonics of MNPs dominated by Brownian relaxation. The difference in the AC magnetization response and magnetization harmonic between the Fokker-Planck equation and the Langevin function was analyzed, and we studied the relationship between the magnetization harmonic and the key factors, such as Brownian relaxation time, temperature, magnetic field strength, core size and hydrodynamic size of MNPs, excitation frequency, and so on. We proposed a compensation function for AC magnetization harmonic with consideration of the key factors and the difference between the Fokker-Planck equation and the Langevin function. Then a temperature estimation model based on the compensation function and the Langevin function was established. By employing the least squares algorithm, the temperature was successfully calculated. The experimental results show that the temperature error is less than 0.035 K in the temperature range from 310 K to 320 K. The temperature estimation model is expected to improve the performance of the magnetic nanoparticle thermometer and be applied to magnetic nanoparticle-mediated hyperthermia.