The invention relates to a data storage method and data storage system for a self-contained application, and belongs to the marine instrument field. According to the method, a plurality of SD/TF cardsare mapped into a virtual SD/TF card, collected data are sequentially written into the SD/TF cards in turn for storage; for the whole system, the write-in process is that the data is sequentially andalternately written into the SD/TF cards, the throughput of the SD/TF cards is fully utilized, and stable SD/TF card write-in performance is obtained to the maximum extent; and the data of the same file is written into each SD/TF card in parallel in a partitioning manner, so that the parallel reading through the multi-card controller can be supported in the subsequent reading process from the computer host. A required file system is unifiedly constructed, the data can be directly read by a computer, the reading process can be read from a plurality of SD/TF cards in parallel, and the data exporting speed is higher.