Along with the horizontal project volume raising, lots of problems have been exposed during the course of practice, which affect its comprehensive value in colleges and universities. According to the investigation on the current situation of horizontal projects, it was found that the main factors which affect the quality of horizontal project management are operational management, funds management and evaluation mechanism. In order to prevent the horizontal projects from being marginalized, the management model should be more adapted to the market economy, with flexible and precise regulations of funds, and be more valued in the personnel evaluation system. Besides, education is another useful resource which has a great effect on the horizontal projects. With the improvement of management, the horizontal projects will be able to further the development of research and technology promotion in universities.