The invention discloses a method for analyzing important metabolites related to sulfur metabolism in a biological sample. According to the method, a capillary electrophoresis-time of flight mass spectrum hyphenated technique is utilized; firstly, a plurality of samples are fed into capillaries by a multi-sampling mode; then pH difference between a sample matrix and background electrolyte is utilized to achieve online enrichment through large-volume sample injection and sample injection interval control. The method improves detection flexibility through online enrichment; meanwhile, the multi-sampling mode greatly shortens analyzing time, improves detection throughput and also effectively reduces method developing time. The analyzing method disclosed by the invention has the advantages of simple pretreatment process, quick analysis, high throughput, high flexibility, good repeatability and the like.