The invention relates to an NGS-based chromosome equilibrium translocation detection and analysis system and application, and belongs to the technical field of gene detection biological information. The detection and analysis system comprises a data acquisition module, a genome comparison module, a sliding cutting module, a short sequence comparison module, a breakpoint analysis module and a result output module. Firstly, reads which cannot be simultaneously compared to a human reference genome at two ends are screened out and cut into continuous short sub-sequences by sliding; the sub-sequences are compared to the human reference genome again, so that the reads sequence originally comprising balanced translocation points can be compared with the human genome through short fragments aftercutting; and through clustering grouping of comparison positions and a correlation covariance weighting algorithm of corresponding sub-sequence numbers, reads of which the two ends are respectively compared with different chromosomes can be quickly screened out, and a balanced translocation breakpoint is accurately positioned, so that a sequence designed by a primer is provided for subsequent Sanger sequencing verification. The application range comprises NIPT, PGS, PGD, common NGS sequencing results and the like.