By using plan-view and cross-sectional transmission electron microscopies and Rutherford backscattering and channeling spectroscopy technologies, the secondary defect in MeV P+-implanted Si and the effect of self-ion irradiation on them have been investigated. The experimental results showed that the depths of secondary defect peaks are a little bit larger than the mean projected ranges measured and those computed by using program TRIM. The results also pointed out that the self-ion irradiation onto the MeV P+-implanted Si with a suitable energy and dose before annealing can reduce the secondary defect formation. But if the self-ion irradiation is applied after the annealing, the effects will be contrary. The physical reason of these has been discussed. Furthermore, the critical dose of the secondary-defect occurring in Si+- and P+-implanted Si have been presented, and the relation of the critical dose with the ion-implantation energy has been also discussed.