Side-chain fluorination of nonfullerene acceptors (NFAs) has been rarely reported to enhance their photovoltaic performance, although it may improve their backbone organization and carrier mobilities. Here, we design new partially fluorinated side chains and incorporate them into M-series NFAs, which are featured with a ladder-type heteroheptacene-cored skeleton without sp3-hybridized carbons. Compared with the traditional M-series acceptor with non-fluorinated side chains (MC7F0), the NFA with partially fluorinated side chains (MC7F3) shows down-shifted energy levels, reduced miscibility, and more importantly, improved backbone organization, thereby leading to the formation of a 3D network packing structure with enhanced carrier transport. Consequently, the MC7F3-based device exhibits a power conversion efficiency of 17.61% and an excellent fill factor of 79.48%, both of which are among the best values for all A-D-A-type NFAs reported so far. The results highlight that side-chain fluorination can efficiently enhance π-conjugated backbone organization, improve intermolecular interaction, increase electron mobilities, and boost photovoltaic performance of NFAs.