In this paper, we justify the semi classical limit of Gross-Pitaevskii equation with Dirichlet boundary condition on the 3-D upper space under the assumption that the leading order terms to both initial amplitude and initial phase function are sufficiently small in some high enough Sobolev norms. We remark that the main difficulty of the proof lies in the fact that the boundary layer appears in the leading order terms of the amplitude functions and the gradient of the phase functions to the WKB expansions of the solutions. In particular, we partially solved the open question proposed in \cite{CR2009, PNB2005} concerning the semiclassical limit of Gross-Pitaevskii equation with Dirichlet boundary condition. (This is a joint work with Gui Guilong).