A newly constructed optical measurement system was introduced to nondestructively measure the composition of the inside of an apple by time-of-flight near-infrared spectroscopy (TOF-NIRS). As sugar content increased, optical parameters concerned with time-resolved profile of transmitted pulsed light (the attenuance of peak maxima, At, the time delay of peak maxima, Deltat, and the variation of full width at half-maximum, Deltaw) decreased gradually. When the acid content increased, At and Deltaw increased; however, a significant tendency could not be found for Deltat. At, Deltat, and Deltaw were employed as the explanatory variables for multiple linear regression, principle component regression, and partial least-squares analysis. It was possible to predict both sugar and acid contents in an apple with high precision by TOF-NIRS. Especially, the superiority of TOF-NIRS lied in more precise determination of acid content.