Glycosyltransferases are involved in the biosynthesis of oligosaccharides and polysaccharides. They are presented in both prokaryotes and eukaryotes, and play significant roles in biological processes. We deleted the glycosyltransferase homologue gene, sll1466, from Synechocystis PCC 6803. Thin-section electron micrographs showed that the mutant Synechocystis contained more carboxysomes when grown in the absence of CO₃^2- and while more glycogen granules when grown in the presence of 0.5 mol/L NaCl than the wild type Synechocystis. Absorption spectra of the mutant grown under different light intensities differed significantly from wild type Synechocystis. At the molecular level, the mutant differed from the wild type in 3 aspects: (1) glycosylation of two carbohydrate-selective OprB porins in the thylakoid membrane; (2) phosphorylation of the rod-core linker, CpcG1 (Slr2051), in the supernatant of the thylakoid membrane; and (3) transcriptional variations of genes related to the above changes. These results suggested a profound role for Sll1466 in regulating physiology, metabolism, and energy transfer.