Currently, arginine-rich cell-penetrating peptides (CPPs), due to their little cytotoxicity and high transmembrane efficiency, are considered as one of the important intracellular carriers. Although the mechanism of the transmembrane process for arginine-rich CPPs was proposed, the quantitative correlations and the key factors involved in this process still deserve further investigation. In this study, all-atom molecular dynamics and the umbrella sampling technique were employed to study the arginine-rich CPPs transmembrane process. In the adsorption process of CPPs from solution to the surface of the lipid bilayer, the adsorption free energy (Delta G(A)) is found to be linearly related to the interaction energy change (Delta E-A): Delta G(A) = 0.0426 Delta E-A + 36.7, R-2 = 0.92. In the CPPs transmembrane process, the transmembrane free energy barrier (Delta G(B)) is roughly correlated with the corresponding interaction energy change (Delta E-B): Delta G(B) = 0.108 Delta E-B + 135, R-2 = 0.73. The multiple salt bridges of guanidinium-PO4 account for 65% of the overall interaction energy, so the increased negative charges of the lipid bilayer or more salt bridges would facilitate CPPs adsorption and transmembrane processes. Also, the increased negative charges of the lipid bilayer would reduce the amount of water to be carried into the pore and further reduce the Delta G(B). The peptide backbone would not have a direct impact on transmembrane efficiency. The Delta G(B) is also found to be related to the length of the pore (L): Delta G(B) = 46.2L - 31.3, R-2 = 0.92, which makes the transmembrane efficiency estimable. This work is expected to deliver an in-depth understanding and help the optimization of CPPs.