This study analyzes the instantaneous spatial energy density and Poynting vector in the WPT system and presents time-varying distributions and animations of this energy density and Poynting vector. First, the energy density is decoupled by two self-energy densities of each coil and the mutual energy density of the two coils. Result reveals how the energy is stored in the WPT system. Second, the Poynting vector is analyzed, and it is found that the power is transferred only in the last half period of the Poynting vector, not at every moment of the whole period. This instantaneous Poynting vector also possesses a characteristic that shows no power flow on the condition that the current phase difference equals zero. This finding is different from the energy density and indicates that the instantaneous Poynting vector can perfectly interpret how power is transferred in the WPT system. Finally, a simulation and an experiment were conducted to verify the correctness of the analysis. This study contributes to a deeper and better understanding of the intrinsic characteristics of energy storage and power flow in the WPT system, and can be referred to for WPT system design and optimization when one considers the EMC or human electromagnetic field exposure problem.