A measurement method of nanoparticle sizes by the variance of temporal coherence of dynamic light scattering was presented to resolve problems of complex algorithms, slow operation, and high costs of traditional dynamic light scattering nano-particle measurement systems and its algorithm and measurement system were studied, respectively. Firstly, the photon correlation spectroscopic theory of dynamic light scattering measurement was introduced, and the concept of coherence degree which includes a temporal coherence factor and a spatial coherence factor was deduced. Then, based on the statistical properties of photoelectric detectors, the variance of the fluctuation of scattering intensity was deduced through analysis of the variance of photon counting. The equations of the variance of intensity fluctuations and the temporal coherence degree were established, and the decay width of a dynamic light scattering signal was obtained by the equations. Finally, the particle diameters of the nano-particles were calculated by the Stokes-Einstein equation.Furthermore, the latex particle sample solution with the diameters of 30, 50, 100 nm and the transmission of 96% was used as the standard sample to be tested in an experiment. The results show that the average values of the measurement error and repeatability error of the new method are 1.84% and 1.76%, respectively, which satisfies the national standard that these errors should be less than 2%, respectively.