The micro abrasive jet machining is used to make the microfluidic channels on the glass substrate. Based on the tests with or without masks, the structure profile and erosion rate with different basic machining parameters, such as nozzle standoff distance, scanning speed, abrasive mass flow rate etc. are investigated. The optimum parameters for micro-structure machining of glass is discussed. The effect of the secondary rebounding particles in mask underetching was analyzed using oblique machining. And the flux effect was also studied comparing with the unmasked machining.