The process of rubber composite armor anti-shaped charge jet (SCJ) penetration was divided into four parts based on jet deformation that occurred when the SCJ penetrated the rubber composite armor. Results on the interference speed interval, interference frequency, and surplus penetration capability of the SCJ with the rubber composite armor were derived based on the stress wave and the Kelvin-Helmholtz instability theory. The effects of rubber layer thickness and obliquity of the armor for the composite armor anti-SCJ penetration were studied through theoretical, X-ray, and depth of penetration experiments. The results showed that when the obliquity was at 60 degrees and the rubber layer thickness was in the range of 3mm to 3.5mm, the rubber composite armor seriously disturbed the stability of the SCJ. Thus, the rubber composite armor was found to have the best protection capability under these specifications.