This paper presents a numerical investigation based on the Lattice Boltzmann method for gaseous flow in a microchannel with rectangular grooves on the walls. Firstly, the prepared computer code is validated with comparison the obtained results with analytic solution for fully developed rarefied gas flow in a simple micro channel. The effects of the rectangular grooves on the flow characteristics and heat transfer behavior are discussed and the results are compared with a simple mircochannel. For this purpose, a two-dimensional constant wall temperature microchannel with air as the coolant is investigated. The results show that the heat removal increases for the grooved channel more than 50% compared with a simple microchannel. But the pressure drop is also increases due to the effects of grooves. The increase in friction factor is more than twice for some Knudsen numbers.