Exploiting micelles of polyethylene glycol–dipalmitoylglycerophosphoethanolamine (PEG–DPPE) as a drug delivery approach is of great promise for improving therapeutic targeting and the half-lives of drugs. To optimize the micelle carriers, pending issues concerning the kinetics underlying the carrier-membrane interplay and the specific contributions of the micelle hydrophobic/hydrophilic components remain to be addressed. Relying on MARTINI coarse-grain (CG) molecular dynamics simulations, we explored the carrier-membrane fusion dynamics of PEG–DPPE micelles with different PEG repetitions in delivering doxorubicin (DOX). A bilayer model composed of 20% phosphatidylglycerol (POPG) and 80% phosphatidylcholine (POPC) was constructed to mimic anionic cancer cell membranes. The CG model of DOX was pioneeringly constructed herein, and it was found to distribute at the hydrophilic/hydrophobic interface of the PEGylated micelles, in agreement with experimental results. The free DOXs cause insignificant disorder of the membrane organization, whereas the PEG–DPPE micelles encapsulating DOX lead to a remarkable membrane invasion supported by the order parameter of the lipid acyl carbon tails and the membrane permeation free energy of DOX. The carrier–bilayer interaction shows a stepwise form attributed to the rearrangement of the zwitterionic/anionic lipids upon the absorption of the DOX-micelle complex on a membrane locality, which initiates the rapid release of DOX to the bilayer interior. Benefiting from the enhanced micelle-membrane interplay, the PEG1250-DPPE micelles result in severe bilayer breakage and deeper membrane insertion of DOX compared to the PEG2000-DPPE micelles. This study provides new theoretical insights into the mechanism of PEG–DPPE micelles in delivering drugs through membranes, which is of benefit for further optimization of PEGylated delivery systems.