Our team previously demonstrated that Ganoderma lucidum spores (GLS) and resistant starch (RS) had hypoglycemic effects separately on type 2 diabetic mellitus (T2DM) rats. This work was to explore the effects of administering encapsulated GLS within RS (referred to as EGLS) in the T2DM rats, which were induced by streptozotocin (STZ). The EGLS was orally administered to rats for 28 days. The parameters of glycometabolism and lipometabolism were evaluated, and fecal microbiota composition was investigated. The results showed that EGLS significantly enhanced glycometabolism and lipometabolism parameters in T2DM rats, which might be associate with the enhancement of the glucose and lipid metabolism, insulin secretion, and glycogen synthesis and reduced lipogenesis. Furthermore, the intervention of EGLS also reduced the Proteobacteria community and improved dysfunctional gut microbiota. This study indicated EGLS may be a potential candidate for dietary intervention to modulate diabetes.