A holding apparatus of a microfluidic device includes a top holder having a coupler and a top casing capable of adjusting the distance and tilt therebetween using three points adjustment. When a microfluidic device along with a cover are disposed on a bottom holder of the holding apparatus and the top holder is pivoted with respect to the bottom holder to a closed position, the contact surface of soft plugs on the coupler and the cover can be made parallel by a certain distance with a first surface of the microfluidic device, and the distance between the coupler and the top casing determines the pressure exerted through elastic components onto the microfluidic device, so that external pipes can be seamlessly attached to the microfluidic device and also ensuring no deformation due to external forces should happen on microfluidic device.