Microfluidic systems have witnessed rapid development in recent years. As one of the most common structures, the micro-orifice is always included inside microfluidic systems. Hydrodynamic cavitation in the micro-orifice has been experimentally discovered and is harmful to microfluidic systems. This paper investigates cavitating flow through a micro-orifice. A rectangular micro-orifice with a l/d ratio varying from 0.25 to 4 was selected and the pressure difference between the inlet and outlet varied from 50 to 300 kPa. Results show that cavitation intensity increased with an increase in pressure difference. Decreasing exit pressure led to a decrease in cavitation number and cavitation could be prevented by increasing the exit pressure. In addition, the vapor cavity also increased with an increase in pressure difference and l/d ratio. Results also show the pressure ratio at cavitation inception was 1.8 when l/d was above 0.5 and the cavitation number almost remained constant when l/d was larger than 2. Moreover, there was an apparent difference in cavitation number depending on whether l/d was larger than 1.