In this paper we define the overflow problem of a network coding storage system in which the encoding parameter and the storage parameter are mismatched. Through analyses and experiments, we first show the impacts of the overflow problem in a network coding scheme, which not only waste storage spaces, but also degrade coding efficiency. To avoid the overflow problem, we then develop the network coding based secure storage (NCSS) scheme. Thanks to considering both security and storage requirements in encoding procedures and distributed architectures, the NCSS can improve the performance of a cloud storage system from both the aspects of storage cost and coding processing time. We analyze the maximum allowable stored encoded data under the perfect secrecy criterion, and provide the design guidelines for the secure cloud storage system to enhance coding efficiency and achieve the minimal storage cost.