Chronic kidney disease management necessitates dietary protein moderation, and rice, a global staple with high glutelin content, may contribute to renal metabolic load. This study investigated the long-term effects of low-glutelin (LG) rice on physiological metabolism and gut microbiota in C57BL/6 J mice fed a control (CON), a normal-glutelin (NG) rice, or a LG diet for eight weeks. The LG diet did not affect growth, organ indices, or kidney morphology but significantly reduced serum low-density lipoprotein cholesterol (0.46 to 0.34 μmol/L) and uric acid levels (175 to 141 μmol/L). Although short-chain fatty acid profiles were similar across groups, 16S rRNA sequencing revealed that the LG diet specifically reshaped the gut microbiota, marked by the enrichment of taxa previously associated with metabolic improvement, such as Dubosiella. These findings demonstrate that long-term LG rice consumption is safe and confers beneficial metabolic effects, potentially mediated through targeted modulation of the gut microbiota, suggesting its potential role as a functional dietary option for metabolic health.