近几年我国高校成为开展横向科学研究的一支重要力量，科研经费也成为学校重要的资金来源之一。但目前高校对横向科研经费的管理还比较粗放，导致横向科研经费使用不规范的现象比较严重。国家虽制定了一些相关管理办法，但项目承担单位内部控制制度涉及和执行还存在有一定的缺陷，这都源于横向科研项目有一定的特殊性和市场性，在项目经费的使用过程中怎样做好既能区别管理又要与现有制度想融合，是个急待解决的问题。 本文使用了文献研究法、观察法、问卷调查法、经验总结法、归纳法和个案分析法等方法，分析了我国现有高校横向科研项目具有能够满足社会市场需求、支持企业发展、增加高校收入的特点，在院校教学、科研中心工作中发挥的积极作用。认为当前横向科研经费管理中存在的对管理办法和经费性质的认识偏差问题、经费内控缺乏合理性和有效性问题。产生的原因主要是结题审计环节随意。从项目负责人和管理人员看待问题的角度设计了两套问卷进行调查，发现管理中存在缺乏绩效评估制度和经费使用责任追究制度方面不完善的问题，最后，从明确高校应建立健全内部控制制度；建立高校科研经费使用效益后评估制度；建立高校科研经费使用责任追究制度；建立高校横向科研经费的绩效奖励制度等方面提出了相应的对策和建议。

In our country, colleges and universities have become an important force to carry out the horizontal scientific research in recent years, and research funds have become one of the important sources of funds for them. However, the management of horizontal scientific research funds is relatively extensive, which leads to the nonstandard of using fund widespread. In spite of some relevant national policies, the particularity and marketability of horizontal scientific research brought some controlling and execution shortcomings to the involving units. It is a problem to be solved urgently how to differentiate management of project funds and integrate with the existing system at the same time. tific research, like satisfying the market demand, supporting the development of the enterprise, and increasing the income of the university. It also states management status of horizontal scientific research and the active roles in the scientific research work. Currently, the existing problems in the horizontal scientific research management include the deviation of conception of management methods&funds and the lack of rationality&effectiveness of internally piloting. The reason that random of project measurement&audit and lack of performance evaluation system and using system of accountability have been carried on a further analysis. From the angle of the project director and managers, two sets of questionnaires to investigate have been designed. Aimed to solve these problems, it is clear that colleges&universities should put forward some corresponding countermeasures and suggestions to establish a sound system of internal control and the efficient use of scientific researchWith the methods of literature, observation, questionnaire investigation, experience summary, induction and case analysis, the paper analyzes the characteristics of the transverse scien after evaluation system, build the responsibility system of scientific research and establish performance incentive system.