In this work, an ultra-high throughput microfluidic particle counting system is demonstrated. For the particle counting, a low cost custom-design optical hardware is developed. The microfluidic chip utilizes the inertial microfluidics to focus the particles in a certain location which significantly enhanced the optical signal utilized for the quantification of the number concentration. The effect of the particle focusing on the counting performance is demonstrated. The proposed system has a potential to be portable and has a capability to process 10 ml of sample within couple minutes.