The molecular structure of the donor and acceptor materials not only has a decisive effect on the photoelectric conversion efficiency(PCE) of polymer solar cells, but also has an important impact on their stability. In this paper, three similarly structured A-D-A acceptor small molecules(FBR, IDFBR, and IDTBR) were blended with P3 HT to explore the influence of molecular structure on cell stability, aiming at resolving the effect of the π-conjugated unit of non-fullerene acceptor(NFA) molecules on devices stability. IDFBR and IDTBR were obtained by thickening the π-conjugated core of FBR with benzene ring(IDFBR) and thiophene ring(IDTBR). Results indicate that IDFBR and FBR have similar absorption spectra and optical band gaps, while IDTBR has a narrower optical band gap. Atomic force microscopy and X-ray diffraction analyses confirm the large P3 HT nanocrystals in P3 HT:IDFBR blend film, while IDTBR and FBR are well mixed with P3 HT, forming co-crystals. The IDFBR-based cell shows higher open circuit voltage(VOC, 0.86 V), while the IDTBR-based cell shows higher short circuit current(JSC, 12.41 mA/cm2). A highest PCE of 5.80% is obtained for P3 HT:IDTBR cell. More importantly, the IDTBR based cells show extremely good device stability. The devices did not decay after continuously illuminating for 500 h. The present work proves that P3 HT:IDTBR is a promising polymer solar cell system that has a good balance of efficiency, cost, and stability.