The invention discloses a data processing method of a next-generation sequencing (NGS) data analysis platform (IMP). The next-generation sequencing data analysis platform implements an entire next-generation sequencing processing process as a single step from inputting of short-reading long-sequences of an FASTQ file format to outputting of mutation detection of a standard VCF file format; at thesame time, the method also provides an option of outputting an intermediate result of sequence alignment in a standard SAM or BAM format; longer data searching and loading time required for I/O accessing of hard drives and SSDs can be avoided through massive memory accessing without using slow I/O to exchange data; hash table writing or reading, deletion of duplicated alignment records and mutation detection are all enabled to be faster; quick next-generation sequencing data analysis can be realized on the premise of not impacting analysis quality; and compared with speeds of existing schemes,a speed of the method is increased up to 20 times.