The bulk morphology of the active layer of organic solar cells (OSCs) is known to be crucial to the device performance. The thin film device structure breaks the symmetry into the in-plane direction and out-of-plane direction with respect to the substrate, leading to an intrinsic anisotropy in the bulk morphology. However, the characterization of out-of-plane nanomorphology within the active layer remains a grand challenge. Here, we utilized an X-ray scattering technique, Grazing-incident Transmission Small-angle X-ray Scattering (GTSAXS), to uncover this new morphology dimension. This technique was implemented on the model systems based on fullerene derivative (P3HT:PC BM) and non-fullerene systems (PBDBT:ITIC, PM6:Y6), which demonstrated the successful extraction of the quantitative out-of-plane acceptor domain size of OSC systems. The detected in-plane and out-of-plane domain sizes show strong correlations with the device performance, particularly in terms of exciton dissociation and charge transfer. With the help of GTSAXS, one could obtain a more fundamental perception about the three-dimensional nanomorphology and new angles for morphology control strategies towards highly efficient photovoltaic devices.