To differ from the usually applied Eulerian method for describing the motion of fluid, the governing equations complete in the Lagrangian form for describing three-dimensional progressive and short-crested waves system are derived in this paper. A systematical ordering expansion by an appropriate perturbation approximation is developed, and the exactly satisfactory solutions in a form of functional, up to third-order progressive waves and up to second-order short-crested waves, are obtained. The kinematic properties of the waves, including the surface profile, pressure, the paths of fluid particles, and the mass transport velocity, are then described directly. The obtained solution for the short-crested waves system is successfully verified by reducing to two special cases, one is the two-dimensional simple progressive waves, and the other is the two-dimensional standing waves. Also, the analytical results are compared with experimental data including the surface profiles, the pressures and the paths of fluid particles for validation.