In this paper, we propose a lattice Boltzmann BGK model for simulation of micro flows with heat transfer based on kinetic theory and the thermal lattice Boltzmann method (He et al., J. Comp. Phys. 146:282, 1998). The relaxation times are redefined in terms of the Knudsen number and a diffuse scattering boundary condition (DSBC) is adopted to consider the velocity slip and temperature jump at wall boundaries. To check validity and potential of the present model in modelling the micro flows, two two-dimensional micro flows including thermal Couette flow and thermal developing channel flow are simulated and numerical results obtained compare well with previous studies of the direct simulation Monte Carlo (DSMC), molecular dynamics (MD) approaches and the Maxwell theoretical analysis.