Kidney stones, often resulting from a complex interplay of factors including oxalic acid, uric acid, and calcium. Current treatments lack comprehensive consideration of these factors and come with side effects. In this study, Lactobacillus paracasei GR-10 and Pediococcus acidilactici GR-11 were isolated from the fermented food “Jiangshui”. GR-10 demonstrated the ability to degrade 62.70% of oxalic acid (10 mM) within 24 h, while GR-11 degraded 28.60% of uric acid (4 mM). Combined treatment with GR-10 and GR-11 significantly reduced the number of stones in rats with ethylene glycol-induced kidney stones. This reduction was accompanied by a 57.19% decrease in urinary oxalate and a 52.80% decrease in serum uric acid levels. Simultaneously, urinary calcium level decreased by 27.18%. Inflammatory markers and indicators of oxidative stress associated with kidney stones were restored. Furthermore, the combined treatment effectively regulated the microbiota imbalance induced by kidney stones, resulting in reduced purine nucleoside accumulation in rat feces. This study offers promising insights into probiotics as an adjunct therapy for the prevention of kidney stones in the future.