Gut dysbiosis has been implicated in the progression of chronic kidney disease (CKD), yet the functional alterations of the microbiome and their links to host metabolism in feline CKD pathophysiology remain unclear. Our previous findings suggested that mix (Lm) may mitigate CKD progression by modulating gut microbiota composition and restoring microbial balance. In this pilot study, we aimed to evaluate the potential effects of an 8-week Lm intervention in cats with stage 2-3 CKD and to investigate the underlying host-microbiota interactions through integrated multi-omics analysis. We performed full-length 16S rRNA amplicon sequencing and untargeted metabolomics to characterize the intricate interactions between the gut microbiome and host metabolome, and further investigate the modulation of microbial function and its related gut-derived metabolites before and after the intervention. During this period, creatinine and blood urea nitrogen levels were stabilized or reduced in most cats, and gut-derived uremic toxins (GDUTs) showed modest numerical reductions without statistically significant changes. Lm intervention was also associated with increased gut microbial diversity, alterations in specific bacterial taxa, and upregulation of microbial functions involved in GDUTs and short-chain fatty acid (SCFAs) biosynthesis pathways. To further explore individual variations in response, we conducted a exploratory subgroup analysis based on changes in microbial-derived metabolites. Cats classified as high responders, defined as those with reductions in three GDUTs and increases in SCFAs, exhibited distinct microbiome compositions, microbial functional profiles, and metabolite shifts compared to moderate responders. Among high responders, modulation of microbial pathways involved in GDUTs (tyrosine, tryptophan, and phenylalanine metabolism) and SCFAs (pyruvate, propanoate, and butanoate metabolism) biosynthesis was particularly evident. Notably, the relative abundance of Lm strains was higher in high responders, suggesting a potential association between colonization efficiency and microbial metabolic outcomes. This study demonstrates an Lm-mediated interconnection between the modulation of microbial composition, metabolic functions, and systemic metabolite profiles. Overall, our findings suggest that Lm intervention may influence the gut-kidney axis in cats with CKD. These preliminary, hypothesis-generating results highlight the value of multi-omics approaches for understanding host-microbe interactions and support further investigation into personalized probiotic strategies as potential adjuvant therapies in feline CKD.