We report a pronounced thickness effect of bulk heterojunction (BHJ) layers on the performance and stability of inverted polymer solar cells with the BHJ layers of poly[(4,8-bis(5-(octylthio)thiophen-2-yl)benzo[1,2-b:4,5-b′]dithiophene-co-3-fluorothieno[3,4- b]thiophene-2-carboxylate] (PBDT-TS1) and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM). The thickness of the BHJ layers was varied from 40 to 120 nm by changing solution concentrations and spin-coating speeds. The results showed that the film thickness considerably affected the performance and stability of devices. The power conversion efficiency reached ca. 9% at the thickness of 80 nm by the optimized nanoscale phase separation between donor and acceptor components. However, the devices with 120 nm-thick BHJ layers showed better device stability under continuous illumination with a simulated solar light due to the well-maintained surface morphology and nanostructure in addition to the improved morphological volume stability.