Acceptor-Acceptor′-Acceptor (A-A′-A) type perylene diimide (PDI)-based dimeric non-fullerene electron acceptors (NFEAs) have drawn the special attention but have not been sufficiently exploited. With that in mind, two A-A′-A type NFEAs, DTBT-(PDI-HD)2 and DTFBT-(PDI-HD)2, in which 4,7-di(thien-2-yl)benzo[c][1,2,5]thiadiazole (DTBT) and its monofluorinated 4,7-di(thien-2-yl)-5-fluorobenzo[c][1,2,5]thiadiazole (DTFBT) as central linkers, both N,N′-(2-hexyldecyl)-PDI (PDI-HD) units as flanked biwings, were successfully synthesized to probe into the influence of different electron-deficient linkers on thermo- and photo-stability, absorption, energy level, molecular configuration, exciton dissociation, charge mobility and solar cell performance. Both A-A′-A type acceptors with excellent thermal- and photo-stability possessed the complementary absorption ranging from 300 nm to 780 nm and matched ELUMO of −3.84 eV to −3.91 eV when pairing with PTB7-Th. Moreover, increased molecular dipole moment, slightly blue-shifted the maximum absorption peak, decreased the absorption coefficient and deepened the ELUMO were found after monofluorinating the benzothiadiazole. Conversely, the augmented aggregation both in solution and film effectively tuned the miscibility and morphology of active layer, contributing to the improvements of the exciton dissociation, charge mobility and photocurrent. Benefiting from this, monofluorinating the electron-deficient benzothiadiazole linker made the JSC increase from 3.72 to 7.19 mA cm−2, the FF enhance from 34.99 % to 38.18 % in DTFBT-(PDI-HD)2-based device when blending with PTB7-Th, contributing to 1.09 times increased PCE from 1.03 % to 2.15 % even in the adverse condition of 0.01 V dropped VOC. These results suggest that monofluorinating the electron-deficient benzothiadiazole linker is an effective approach for boosting the device efficiency via tuning the molecular aggregation and affecting the related morphology and charge mobility during the A-A′-A type PDI-based NFEAs.