The invention relates to a method for high-throughput analysis of single cell inclusions by using a paired micro-fluidic chip. The paired micro-fluidic chip is the micro-fluidic chip for high-throughput capturing single microspheres/single cells. The method comprises the steps of (1) carrying out high-throughput pairing capturing on single microspheres/single cells; (b) carrying out parallel control on a pairing unit, for example, isolation, cultivation and pyrolysis of a lot of single cells, and capturing of various inclusions in the single cells; and (c) converting information of the single cell inclusions into DNA sequence information through encoding the microspheres, analyzing a lot of single cell inclusions, such as a transcriptome, a genome, an miRNA, a proteome, a methylated DNA, a metabolite, a lipidosome and phospholipid by adopting a high-throughput sequencing technology and a bioinformatics method. According to the method, the single cell inclusion information can be comprehensively and completely analyzed, and the method has the advantages of high throughput, high accuracy, low cost and wide analyzable target.