The bulk heterojunction (BHJ) morphology of photovoltaic materials is crucial to the fundamental optoelectronic properties of organic solar cells (OSCs). However, in the photoactive layer, the intrinsic crystalline packing structure of Y6, currently the hallmark molecule among Y-series non-fullerene acceptors (NFAs), has not been unambiguously determined. Here, employing grazing-incidence wide-angle X-ray scattering (GIWAXS), we managed to uncover the intrinsic crystalline packing structure of Y6 in the BHJ active layer of OSCs, which is found to be different from its single-crystal structure reported previously. Moreover, we find that solvent additive 1-chloronaphthalene (CN) can induce highly ordered packing of Y6 in BHJ thin films. With the help of atomistic molecular dynamics simulations, it is revealed that pi-pi interactions generally exist between naphthalene derivatives and IC terminals of Y6 analogues, which would essentially improve their long-range ordering. Our work reveals the intrinsic crystalline packing structure of Y6 in the BHJ active layer as well as its crystallization mechanism in thin films, thus providing direct correlations between this crystalline packing and the device characteristics and photophysical properties.