Graduation project is an important education practice for undergraduates of environmental engineering, and it also plays a key role for the cultivation of creative and innovative professionals for new engineering nowadays. An investigation of graduation project for environmental engineering undergraduates in recent 5 years were made in Chongqing University as well as the requirement of employers for them. A new education method for graduation project of environmental engineering has been presented and put into practice based on two supervisors and application of advanced technology and method, and the objective is to aid the innovation of education method and enhance the cultivation of professionals for new engineering.