Lipases have wide applications using as biocatalyst in numerous biotechnological and bioengineering fields, especially function at hydrophobic or amphiphilic interface. Previously, the lipase from Burkholderia ambifaria YCJ01 was significantly activated when immobilized on the amphiphilic environment. In this work, insights into the functional effect of amphiphilic surface on lipase activation are presented by molecular dynamic simulations. The notable open of “lid” (α5 region) and the displacement of “flap” region (α8 region) of the lipase are closely related with the activation mechanism of lipase, which makes the active site accessible. Strikingly, the hydrophobic analysis showed that most of the hydrophobic surface residues of lipase, as an interfacial enzyme, located at the “lid” and “flap” regions make the entry to active site naturally orient to the oil-water interface to achieve enzyme activation. Additionally, the analysis of Rg and hydrogen bonding interaction suggested that the amphiphilic environment benefits to the exposure of hydrophobic regions, especially the “lid” and “flap” regions, and the maintenance of the nonpolar environment of the active site. Observations from this work not only complement the activation mechanism of lipase induced by the amphiphilic environment, but also provide a reference for the engineering of immobilized media for interfacial enzyme.