Conventional on-board storage systems are often weighty, large and high power consumption, which can’t meet the requirement of the miniature airborne synthetic aperture radar (SAR) system. A new data storage system, integrated with SAR signal processor, is presented in this paper. The compact flash (CF) card and the FPGA are used as storage medium and the host respectively, in the data storage system. However, the major problem of high speed data storage is the irregular write response time due to the internal overhead in the card and frequently cluster switching involving retrieving and updating of cluster connection information. Two methods are presented in this paper to solve the problem. The first one is that the DDR3 flashes connecting with the DSP are iteratively used as the buffer of the SAR data. Another method is that all the available clusters are pre-allocated at once when the files are created. To verify our proposal, the prototype data storage system is implemented on a signal processing board and a CF card with the capacity of 128 GB. The added size, weight, and power consumption for the data storage are really small. Moreover, the data writing rate is over 100 MB/s. As a consequence, the system achieves our goal successfully in that storage system of the miniature SAR is compact, high speed and large capacity.