Thermal accommodation coefficient, one of the fundamental parameters in rarefied gas dynamics, is usually introduced to account for the fraction of incident molecules interacting with solid surface in a diffusive manner. In the present study, the effects of thermal accommodation on the unsteady one-dimensional micro-flow are examined, when the oscillating flow input are applied, by employing the unsteady DSMC technique. Since the temperature jump relation has been usually accepted as the thermal boundary condition in the analysis of MEMS flow, it is also focused on in this study. To this end, the wall heat fluxes are also obtained indirectly by applying the temperature jump relation to DSMC temperature profiles. For the case of small system with full thermal accommodation, the indirect wall heat fluxes calculated using the DSMC and free molecular approximation are almost exactly overlapped whereas two direct results show an obvious deviation, because the propagation speed of heat is different. A variation in the thermal accommodation coefficient is observed to only affect the wall properties such as heat flux and wall pressure rather than flow properties. In addition, the difference between indirect and direct heat flux remained being unchanged even if the thermal accommodation coefficient is varied. These aspects need to be kept in mind when analyzing the problem with the temperature jump boundary condition. (C) 2003 Elsevier Ltd. All rights reserved.