This paper presents a thorough comparison between a phase-based and an intensity-based optimization method for 3D shape measurement with the binary dithering techniques. Since for a 3D shape measurement system utilizing digital fringe projection techniques, the phase quality ultimately determines the measurement quality, and thus these two methods are compared in phase domain. Both simulation and experiments find that the phase-based optimization method can generate high-quality phase under given conditions. However, this method is sensitive to the amount of blurring (or defocusing). On contrast, the intensity-based optimization method can consistently generate high-quality phase with various amounts of defocusing. Both experiments and simulations will be presented to compare these two optimization methods