Accurate measurement of the net charge on nanoparticles is critical in research and practical applications. We proposed a method for accurately measuring charge through thermally and harmonically driven motion signals. Our direct-charge-calculation method achieves accuracies of better than 5% at thermal equilibrium pressures of more than 10 mbar and approximately 20% for pressures as low as 3 mbar. This method can improve the measurement accuracy for mass and density through iterations and provide a direction for non-contact characterization of atmosphere and space dust.