As the main force of rural financial market, the rural credit cooperatives bear the functions of serving the county economy, supporting agricultural development and helping small and micro enterprises. The liberalization of deposit rates marked the basic completion of China's liberalization of interest rate, which will bring greater impact on the management of rural credit cooperatives. Combing the characteristics of the management of rural credit cooperatives, this paper analyzes the positive impact on the rural credit cooperatives of elimination control of the deposit interest rate such as promoting the adjustment of business method and transformation to rural commercial bank, also the negative impacts such as narrowing the interest margin, increasing the interest rate risk and so on. Finally, the paper puts forward some countermeasures such as strengthening the traditional business, accelerating the construction of process banks and seeking policy support and so on to deal with the deposit rate liberalization.