Small-molecule donor:polymer acceptor (SMD:PA) organic solar cells have garnered attention due to their excellent active layer stability, yet their efficiency remains significantly lower than other OSC types. This study addresses the challenge of morphology control in SMD:PA systems via a layer-by-layer (LBL) process to optimize the donor–acceptor interpenetrating network. Using small-molecule donor B1 and polymer acceptor PY-IT with chloroform as a universal solvent, we systematically investigated the impact of LBL processing on the active layer morphology and device performance. The inverted LBL device (ITO/ZnO/PY-IT/B1/MoO3/Ag) achieved a power conversion efficiency of 8.6%, significantly outperforming the bulk heterojunction devices (inverted 2.91% and normal 6.11%) and previously reported LBL SMD:PA cells (1.12%). Static and femtosecond transient absorption spectra, time-resolved photoluminescence, and grazing incidence X-ray diffraction analyses revealed that the LBL and nonorthogonal solvent strategy facilitated effective B1 infiltration into the PY-IT layer, forming an optimized active layer with refined phase separation and improved donor/acceptor interfaces, thus resulting in enhanced exciton dissociation and charge transport while reducing recombination losses. This work validates the feasibility of LBL processing for high-efficiency SMD:PA OSCs, offering a novel strategy to overcome the efficiency limitations of this class of OSCs.