Physicochemical properties of endosperm starches in milled rice determine its cooking and eating quality. Amylose is synthesized by granule-bound starch synthase I (GBSSI), whilst amylopectin is synthesized by the synergistic activities of starch synthases (SSs), branching enzymes (BEs) and debranching enzymes (DBEs). However, the complexes formed by starch biosynthetic enzymes are not well characterized. Gene expression profiles and protein complexes were determined in white-core (GM645) and waxy (GM077) mutants derived from a high amylose indica rice Guangluai 4 (GLA4). In GM645, genes including AGPS1, GBSSI, SSIIa, BEI, BEIIa, BEIIb, PUL, ISA1 and SP were significantly downregulated during seed development. In GM077, the expression levels of AGPL2, AGPS1, AGPS2b, SSIIIa, BEI, PUL and ISA1 were significantly upregulated. Co-immunoprecipitation assays revealed interactions of SSs-BEs, SSs-PUL and BEs-PUL in developing seeds. However, weak SSI-SSIIa interaction was detected in GM077, whilst SSI-PUL interaction was absent. Weak interaction signals for SSI-SSIIa, SSIIa-BEI, SSIIa-BEIIb, BEI-BEIIb and SSI-BEI were also observed in GM645. These results suggest that the protein-protein interactions for starch biosynthesis are modified in mutants, which provides insight into the mechanisms of starch biosynthesis, particularly in indica rice.