An integral form of diffusion equations and their finite difference time domain (FDTD) analysis have been formulated. The analysis is extended to FDTD analysis with nonuniform grids in three-dimensional (3-D) scattering medium. It has been confirmed that 600 time steps in calculation sequences of the time-resolved reflectance for 3-D medium 80 × 80 × 30 mm3 in volume is completed within 4 seconds by utilizing 23 and 43 mm3 nonuniform cubic grids, when a conventional personal computer with 3 GHz CPU clock is used. The conditions for keeping numerical accuracies comparable to those in 23 mm3 uniform grids are made clear. The proposed analysis greatly reduces time to run and memory space in 3-D scattering medium numerical analysis.