The support of secure deletion on formatting a file system is to make sure that when a file system is formatted, there is no way to get any file content back again. Due to the fast-growing storage capacity, the performance of secure deletion to file systems on resource-constrained flash storage devices has become a critical issue. In contrast to the existing works that take a long time on overwriting/resetting all the file contents of a file system, we propose an efficient secure deletion scheme to securely delete all the contents of a file system without rewriting file contents. Thus, secure deletion to file systems can be efficiently achieved and can be independent of the device capacity and file systems. A series of experiments was conducted with realistic workloads to evaluate the capability of the proposed scheme. The results show that the proposed scheme achieves secure deletion with limited performance overheads in most cases.