Particulate fouling at elevated temperature is a crucial issue for microchannel heat exchangers. In this work, a microfluidic system is designed to experimentally study on the deposition of micro-particles suspended in microchannels, which simulates the working fluid in microscale heat exchangers. We have directly measured the deposition rate of microparticles and found that the number density of deposited particles was monotonically increased with solution temperature when constant flow rate of samples was maintained. Moreover, our results show that pulsatile flow, which was generated by a piezoelectric unit, could mitigate the particulate fouling in microchannels, and the deposition rate was decreased with increasing the frequency of pulsation within a low frequency region. Our findings are expected to gain better understanding of thermally driven particulate fouling as well as provide useful information for design and fabrication of microchannel heat exchangers.