We present a new algorithm based on a Cartesian mesh for the numerical approximation of kinetic models on complex geometry boundary. Due to the high dimensional property, numerical algorithms based on unstructured meshes for a complex geometry are not appropriate. Here we propose to develop an inverse Lax-Wendroff pro- cedure, which was recently introduced for conservation laws [21], to the kinetic equations. Applications in 1D×3D and 2D×3D of this algorithm for Boltzmann type operators (BGK, ES-BGK models) are then presented and numerical results illustrate the accuracy properties of this algorithm.