Moringa seed protein (MSP) was phosphorylated by dry-heating in the presence of pyrophosphate. The antioxidant activity of MSP, including ABTS+ radical scavenging ability, superoxide anion scavenging ability and chelating capacity, was then investigated before and after phosphorylation by dry-heating in the presence of pyrophosphate. Furthermore, the effects of phosphorylation on structure of MSP were identified by spectra fluorescence and circular dichroism spectra. The results showed that the antioxidant activity of MSP slightly increased after heating in a dry environment. However, its antioxidant activity significantly improved by dry heating phosphorylation in the presence of pyrophosphate. In addition, phosphorylation induced a slight secondary structural change in MSP, but remarkably increased its surface sulfhydryl thiol (SH) groups and had no actual effect on its solubility. The improved antioxidant property of MSP can be affected by the introduced hydrophilic phosphate groups and the increase of the surface SH content.