Slicing reference data and adaptive slicing algorithm are the key issues to find out appropriate layer thicknesses of three-dimensional (3D) microstructures with free-form surface in two photon polymerization (TPP). In the present work, an adaptive slicing method (ASM) was proposed to improve the fabricating efficiency of 3D microstructures with free-form surface in TPP microfabrication. In the proposed method, slicing reference data were obtained by intersecting a series of vertical planes with the triangular patch format along characteristic directions. Maximum acceptable chordal height played a role as judging criteria to obtain appropriate layer thicknesses. What’s more, typical 3D microstructures with free-form surfaces were fabricated with uniform slicing method (USM) and the proposed ASM, respectively. The comparison results showed that the proposed method effectively improved fabricating efficiency, guaranteeing an acceptable surface quality at the same time. This work was expected to provide references for improving fabrication efficiency of complex 3D microstructures in TPP.