Renal anemia is one of the most common complications of chronic kidney disease (CKD). This study investigated gut microbiota composition and fecal/plasma short-chain fatty acids (SCFAs) in 30 non-dialysis renal anemia patients and 20 healthy controls. Gut microbiota was assessed by 16S rRNA gene amplification sequencing and SCFAs were measured using gas chromatography-tandem mass spectrometry (GC–MS/MS). Compared with healthy controls, renal anemia patients showed distinct gut microbiota composition, including higher relative abundances of Enterobacterales, Enterobacteriaceae, Escherichia-Shigella, and Escherichia coli, and lower abundance of Lachnospiraceae. Fecal acetic acid was higher in renal anemia patients than in controls (p = 0.049). Plasma acetic acid was also increased in renal anemia patients (p = 0.027), whereas plasma isobutyric acid (p = 0.002) and caproic acid (p = 0.035) were higher in controls. In subgroup analysis, moderately anemic patients had higher fecal isobutyric acid (p = 0.019) and isovaleric acid (p = 0.028) than mildly anemic patients. Specific microbial taxa and SCFAs were correlated with clinical indicators of renal anemia. These findings suggest that renal anemia is associated with gut microbiota dysbiosis and alterations in specific SCFAs in the context of CKD, but further studies with eGFR-matched non-anemic CKD controls are needed to clarify the independent contribution of anemia.