Emerging nonfullerene acceptors (NFAs) with crystalline domains enable high-performance bulk heterojunction (BHJ) solar cells. Thermal annealing is known to enhance the BHJ photoactive layer morphology and performance. However, the microscopic mechanism of annealing-induced performance enhancement is poorly understood in emerging NFAs, especially regarding competing factors. Here, optimized thermal annealing of model system PBDB-TF:Y6 (Y6 = 2,2'-((2Z,2'Z)-((12,13-bis(2-ethylhexyl)-3,9-diundecyl-12,13-dihydro-[1,2,5]thiadiazolo[3,4-e]thieno[2″,3'':4',5']thieno[2',3':4,5]pyrrolo[3,2-g]thieno[2',3':4,5]-thieno[3,2-b]indole-2,10-diyl)bis(methanylylidene))bis(5,6-difluoro-3-oxo-2,3-dihydro-1H-indene-2,1-diylidene))dimalononitrile) decreases the open circuit voltage (VOC) but increases the short circuit current (JSC) and fill factor (FF) such that the resulting power conversion efficiency (PCE) increases from 14 to 15% in the ambient environment. Here we systematically investigate these thermal annealing effects through in-depth characterizations of carrier mobility, film morphology, charge photogeneration, and recombination using SCLC, GIXRD, AFM, XPS, NEXAFS, R-SoXS, TEM, STEM, fs/ns TA spectroscopy, 2DES, and impedance spectroscopy. Surprisingly, thermal annealing does not alter the film crystallinity, R-SoXS characteristic size scale, relative average phase purity, or TEM-imaged phase separation but rather facilitates Y6 migration to the BHJ film top surface, changes the PBDB-TF/Y6 vertical phase separation and intermixing, and reduces the bottom surface roughness. While these morphology changes increase bimolecular recombination (BR) and lower the free charge (FC) yield, they also increase the average electron and hole mobility by at least 2-fold. Importantly, the increased μh dominates and underlies the increased FF and PCE. Single-crystal X-ray diffraction reveals that Y6 molecules cofacially pack via their end groups/cores, with the shortest π-π distance as close as 3.34 Å, clarifying out-of-plane π-face-on molecular orientation in the nanocrystalline BHJ domains. DFT analysis of Y6 crystals reveals hole/electron reorganization energies of as low as 160/150 meV, large intermolecular electronic coupling integrals of 12.1-37.9 meV rationalizing the 3D electron transport, and relatively high μe of 10-4 cm2 V-1 s-1. Taken together, this work clarifies the richness of thermal annealing effects in high-efficiency NFA solar cells and tasks for future materials design.