In recent years, with the increasing importance of agricultural enterprises in China's economy, agricultural enterprises are facing fierce market competition. For such a complex and competitive market, cost management is not only of great significance to the development of agricultural enterprises, but also plays an important role in the accurate statistics of relevant agricultural production indicators, the optimization of industrial structure, and the development of modern agriculture and ecological agriculture. This paper analyzes the problems existing in the cost management of agricultural enterprises in our country based on the company of Guizhou Nayong Yuansheng animal husbandry Co., Ltd. during the internship, puts forward solutions according to these problems, improves the importance of cost management of agricultural enterprises, promotes the process of building a reasonable cost management system of agricultural enterprises, and effectively controls the further realization of agricultural production. The reasonable reduction of unnecessary cost in the process will develop the cost of agriculture from disadvantage to advantage. The problems of cost management in Guizhou Yuansheng animal husbandry Co., Ltd. are as follows: firstly, the employees' awareness of cost management is very weak; secondly, the cost information can not meet the company's management needs; finally, the cost management function is set up in confusion and the cost management system is not perfect. Therefore, in order to ensure the normal operation and development of agricultural enterprises in the complex market, enterprises must establish the systematic concept of enterprise cost management, ensure the effective cost information, use computer technology, establish and improve the cost management system.