Different drill-hole positions may produce different drainage results in low protective coal seams. To inves-tigate this possibility, a 3D stope model is established, which covers three kinds of drill holes. The FLUENT computational fluid mechanics software is used to solve the mass, momentum and species conservation equations of the model. The spatial distributions of oxygen and methane was obtained by calculations and the drainage results of different drill-hole positions were compared. The results show that, from top to bottom, methane dilution by oxygen weakens gradually from the intake to the ret side, and methane tends to float; methane and oxygen distribute horizontally. The high-level crossing holes contribute to better methane drainage and a greater level of control. Around these holes, the methane density decreases dramatically and a ‘‘half circle’’ distribution is formed. The methane density decreases on the whole, but a proportion of the methane moves back to deep into the goaf. The research findings provide theoretical grounds for methane drainage.