The liquid mixing is one of the important functions of the microfluidic chip. The microfluidic liquid mixing method can be divided into the active and passive types. Currently, the mixing efficiency of the passive type is not high and the fabrication process of the active type is complex. Aiming at these problems of the microfluidic mixer, a low cost and high efficient pneumatic microfluidic mixer based on the engraving machine was studied and designed. The computer numerical control engraving machine was used for the microfluidic chip to rapidly process micro molds by PDMS curing, molding, punching, bonding, etc, and the fabrication of the microfluidic mixer was completed. Meanwhile, the pulse air driven model in multi-chamber was studied and designed, and the rapid mixing of trace reagents and samples was achieved efficiently. The experimental results show that the designed active microfluidic mixer can play a role of the convective chaos and significantly improve the mixing efficiency in the micro-scale, which provides an effective technical approach to realize the fabrication of the low cost microfluidic chip and efficient reagent mixing in the MEMS biochemical detection system.