With the assistance of HPLC-ESI-MS/MS,the self-assembly products of serine and histidine penta-coordinated phosphorus compound were separated and identified. The expectative product was seryl-histidine dipeptide,but it was found that there was almost equimolar amount of histidyl-histidine dipeptide as well as seryl-histidine dipeptide. The mechanism was speculated that there was ligand exchange between penta-coordinated phosphoryl serine and histidine in the reaction process. As a result,two types of dipeptide were produced. With the assistance of HPLC-ESI-MS / MS, the self-assembly products of serine and histidine penta-coordinated phosphorus compound were separated and identified. The expectative product was seryl-histidine dipeptide, but it was found that there was almost equimolar amount of histidyl-histidine dipeptide as well as seryl-histidine dipeptide. The mechanism was speculated that there was ligand exchange between penta-coordinated phosphoryl serine and histidine in the reaction process. As a result, two types of dipeptide were produced.