As a starting point of studying the long time behavior of the 3D water waves system in the flat bottom setting, in this paper, we try to improve the understanding of the Dirichlet-Neumann operator in this setting. As an application, we study the 3D gravity waves system and derive a new L 2 − L ∞ type energy estimate, which has a good structure in the L ∞ −type space. In our second paper [16], base on the results we obtained in this paper, we prove the global regularity of the 3D gravity waves system for suitably small initial data.