The invention discloses a contig incorrect connection area identification method based on double-side reading insert size distribution.The contig incorrect connection area identification method comprises the following steps that 1, a contigs set and a double-side reading library are input, and double-side readings of the double-side reading library are aligned to the contigs set by using a sequence alignment tool to obtain an alignment result; 2, double-side supported sparse areas are obtained according to the alignment result and serve as candidate areas for incorrect connection; 3, the candidate areas are extended through distribution testing of the double-side readings, and finally whether the candidate areas are incorrect connection positions or not is judged according to the lengths of the areas; 4, boundaries of the incorrect connection areas are determined.The contig incorrect connection area identification method has higher accuracy, can obviously decrease splicing errors in contig through incorrect site cutting and effectively improves the quality of the contig.