We utilized a unique method, using water to lift-off the polymer blend films for investigating the buried polymer/substrate interface without altering the film properties. The PCBM/P3HT ratios were evaluated using carbon/sulfur (C/S) atomic ratios obtained from XPS analysis, which revealed spontaneous vertical phase separation upon spin-coating, as well as enrichment of the donor and acceptor components at the top and bottom surfaces, respectively. This vertical phase separation is attributed to the surface energy differences of P3HT and PCBM, as well as induced dipole-dipole interactions between PCBM and the substrates. This inhomogeneous phase distribution, with P3HT-rich layer at the metal electrode and PCBM-rich at the ITO side is contrary to the ideal morphology for the regular device structure; however, polymer films with this vertical phase separated morphology are beneficial for charge collection in the inverted configuration. By varying the surface property of the substrate, the distribution of the donor and acceptor materials can be manipulated, and the PCBM (or FPCBM) concentrations at the polymer/Cs2CO3 interfaces are higher than at the polymer/glass or polymer/PEDOT interfaces, indicating increased vertical segregation on Cs2CO3-coated ITO substrates. Our work unveiled the inherent advantage of the inverted configuration, validated by the I-V characteristics and EQE results, with 4.2% PCE and EQE maximum at 72%. This device performance is comparable to the regular structure based on the same system, and provided a promising alternative for structure design flexibility in tandem cell application.