Abstract: The three cavities dielectric wall proton accelerator is systemically simulated by the self-developed 3D particle simulation software. On this basis, the transit time of protons in three cavities shall be calculated and the timing optimization design between cavities shall be achieved. The impressed voltage peak value is 100 kV. The width at top is 1ns and it is 10 ns at half maximum. The thickness of insulation micro reactor is 2.0 cm. The proton initial energy is 40 keV. The tungsten mesh is added to accelerating electrode. The simulation results are the following: When the voltage lasts 6.5 ns, the H+ which goes into high insulation gradient material shall get a maximum 90.84% acceleration efficiency while passing the first cavity, and the corresponding transit time is 5.668 ns. When the voltage triggers in the second cavity 4.5 ns behinds the first cavity, the H+ shall get a maximum 94.77% acceleration efficiency while passing the third cavity, and the corresponding transit time is 3.545 ns. When the voltage triggers in the third cavity 3.0 ns behinds the second cavity, the H+ shall get a maximum 97.30% acceleration efficiency while passing the second cavity, and the corresponding transit time is 3.018 ns. The total time of the maximum energy H+ transiting the three cavities is 12.231 ns. The acceleration efficiency of total H+ is 94.31%. When the proton beam center enters the first cavity and falls behind the pulse voltage trigger in 6.5 ns, with the delay time between first and second cavities, the second and third cavities are 4.5 ns and 3.0 ns respectively. The H+ of proton beams whose lengths are 2.5 ns and 4.0 ns shall be accelerated above 90% and 80% respectively.