Chloroplast thylakoid membranes are the sites of the light reactions of photosynthesis. They are also thought to influence starch granule biogenesis via the thylakoid-anchored protein MAR-BINDING FILAMENT-LIKE PROTEIN 1 (MFP1), but mechanistic understanding is scarce. Here, we report an Arabidopsis (Arabidopsis thaliana) mutant affected in PHOTOSYSTEM II REACTION CENTER W (PsbW), an integral thylakoid membrane protein associated with photosynthetic complexes of PSII. This mutant (psbw-2) was identified in a large-scale mutant screen designed to find proteins that regulate starch granule shape and size because it produces an excessive number of small, irregularly-shaped starch granules. The mutation in psbw-2 causes a glycine-to-arginine substitution in PsbW's transmembrane helix. The resulting PsbWG107R protein remains membrane-associated but has lost its ability to stabilize PSII supercomplexes. In addition, the transgenic expression of this mutated version results in abnormal thylakoid membranes that have drastically enlarged luminal spaces and no longer-form distinct grana stacks, leading to reduced plant growth and impaired photosynthesis. These effects increase with PsbWG107R expression levels but are not observed in the psbw knockout mutant, suggesting that PsbWG107R has acquired an aberrant function. We analyzed psbw-2 mutants also lacking either MFP1 or STARCH SYNTHASE 4 (SS4), a key factor involved in granule initiation and growth. These data suggest that thylakoid distortion is caused by the membrane insertion of PsbWG107R, which in turn affects the initiation and growth of starch granules. Our results reaffirm the link between the thylakoid membrane system and starch formation and highlight the importance of proper thylakoid architecture for plant fitness.