The macro-property of the alloy was gone back to the electronic scale of atomic bonding by using the empirical electronic theory (EET) in solid and molecule and the improved interface TFD theory established based on bond theory and band theory. The investigation of interface bonding feature of the atomic bonding of sequence phase and the atomic bonding at the interface between the matrix and the precipitate in Al-Mg-Si alloy was systematically summed through comparing the bond strength, cohesive energy, interface energy between the precipitate and the matrix. The results show that the most effect of strengthening for the alloy is owing to the β″ phase, the second is the pre-β″ phase; the variation of the cohesive energy and the strongest bond energy can also show the melting point of the alloy, which indicates that the melting points of pre-β″ phase, β″ phase and U1 phase are higher than those of GPZ phases and the matrix. The calculated results of atomic bond strength evolution of precipitates are in good agreement with the experiment results of the strengthening alloy.