Understanding electron transport through a single molecular attached to two electrodes is a fundamental issue in molecular electronics. We investigate the effects of electron-phonon inelastic scattering on the transport properties in a single molecular junction in the regime of quasi-ballistic transport. Particularly, we will discuss the small structures occurred in the I-V characteristics and also the current-induced local heating in electrode-alkanethiol-electrode junction due to electrons scattered by the vibrations of molecule. We find that the inelastic profile displays an odd-even effect with chain length which compares well with experimental results. We also compare local temperatures of alkanethiols from theoretical calculations with the measurement from conducting Atomic Force Microscopy (C-AFM).