Based on scientific research evaluation and automatic project evaluation, research and governance of academic ecosystem has become one of the urgent problems to be solved. The paper studies pollution and destruction of academic ecosystem by applying multidisciplinary investigation of philosophy, sociology, politics, economics, AI and so on. It discovers that pollution and destruction stem from hidden invasion by non-academic community's redundant, ineffective academic order destruction and knowledge barrier. The author thus puts forward the definition of academic ecosystem and new middle class, and achieving academic governance by project automatic evaluation. She also proposes the governance design of intelligent platform construction of project automatic evaluation, social function design of automatic project evaluation, and academic institution remodeling so as to govern the academic ecosystem.