The emerging memory technologies, such as phase change memory (PCM), provide chances for highperformance storage of I/O-intensive applications. However, traditional software stack and hardware architecture need to be optimized to enhance I/O efficiency. In addition, narrowing the distance between computation and storage reduces the number of I/O requests and has become a popular research direction. This paper presents a novel PCMbased storage system. It consists of the in-storage processing enabled file system (ISPFS) and the configurable parallel computation fabric in storage, which is called an in-storage processing (ISP) engine. On one hand, ISPFS takes full advantage of non-volatile memory (NVM)’s characteristics, and reduces software overhead and data copies to provide low-latency high-performance random access. On the other hand, ISPFS passes ISP instructions through a command file and invokes the ISP engine to deal with I/O-intensive tasks. Extensive experiments are performed on the prototype system. The results indicate that ISPFS achieves 2 to 10 times throughput compared to EXT4. Our ISP solution also reduces the number of I/O requests by 97% and is 19 times more efficient than software implementation for I/O-intensive applications.