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In this paper, the structures of three phosphorus-containing organosilicon compounds, including N,N-di-methylenephosphoric acid n-propylamine (DPPA), N,N-di-methylenephosphoric acid aminopropyldimethylsilanol (DPDS), and N, N-di-methylenephosphoric acid aminopropyldimethylsilylene glycol (DPMS), have been designed by using a molecular dynamics simulation method. And the preparation of three phosphorus-containing organosilicon compounds was accomplished experimentally by using raw materials such as bisphenol A-type epoxy organosilicon, n-propylamine and phosphite. The structures of the above several substances were proved by means of characterization such as Fourier infrared spectroscopy, hydrogen NMR , and epoxy value. Molecular dynamics simulation analysis revealed that the bond lengths of N atoms to Si atoms, N atoms to O atoms, and N atoms to were 3.03 Å, 3.05 Å, and 2.85 Å, respectively. Si did not participate in the addition reaction, but the intermolecular interactions caused a change in the chemical environment of Si, which reduced intermolecular distances and made it easier for the phosphorus groups to aggregate. This study is very important for the development of new preparation strategies of phosphorus-containing organosilicon and the promotion of phosphorus-containing organosilicon industry.