Due to their unique optical properties, quantum dots with a shell are important materials for many areas of nanotechnology and bionanotechnology. In this work, a method of self-consistent electron-deformation coupling was developed for quantum dot—human serum albumin bionanocomplexes, within which the deformation effects in the CdSe-core/ZnS/CdS/ZnS-shell quantum dots interacting with human serum albumin, which is important for application in nanomedicine, were investigated. The proposed model self-consistently takes into account the mismatch of lattice parameters of contacting materials, the Laplace pressure, the electrostatic interaction and the interaction of the electronic subsystem with the elastic field of the quantum dot, as well as the external pressure caused by the interaction of the quantum dot and the bioobject. Within the framework of the developed model, it was found that QDs with a three-layer shell are more sensitive to deformation and, at the same time, the deformation is almost independent of the core radius. It is shown that, in contrast to CdSe/human serum albumin bionanocomplexes, significant deformations arise in the CdSe/ZnS/CdS/ZnS/human serum albumin bionanocomplexes, which can lead to the energy shift of the edge of conduction band by 40 meV. This result can be used for the development of bionanosensors for the determination of albumin concentration based on CdSe semiconductor QDs with a ZnS/CdS/ZnS multilayer shell.