Environmental microbiology is a compulsory course for environmental engineering major, this course is very important for cultivating student’s applied technology ability and improving the comprehensive quality. The traditional teaching mode has limited the applied technology talents cultivation. The teaching reform ideas and measures of environmental microbiology have been detailed mainly from the theory teaching, experiment teaching, teaching form and teaching construction. This exploration aims at improving student’s applicability understanding for this course and providing the exploration and practice for enhancing the applied technology talents cultivation.