ObjectiveTo confirm the causality of gut microbiota pathway abundance and knee osteoarthritis (KOA). MethodsMicrobial metabolic pathways were taken as exposures, with data from the Dutch Microbiome Project (DMP). Data on KOA from the UK Biobank were utilized as endpoints. In addition, we extracted significant and independent single nucleotide polymorphisms as instrumental variables. Two-sample Mendelian randomization (MR) analysis was applied to explore the causal relationship between gut microbiota pathway abundance and KOA, and MR-Egger and weighted median were used as additional validation of the MR results. Meanwhile, Cochran Q, MR-Egger intercept, MR-PRESSO, and leave-one-out were used to perform sensitivity analyses on the MR results. ResultsMR results showed that enterobactin biosynthesis, diacylglycerol biosynthesis I, Clostridium acetobutylicum acidogenic fermentation, glyoxylate bypass and tricarboxylic acid cycle were the risk factors for KOA. (OR = 1.13,95%CI = 1.04–1.23;OR = 1.12,95%CI = 1.04–1.20;OR = 1.14,95%CI = 1.04–1.26; OR = 1.06,95%CI = 1.00–1.12) However, adenosylcobalamin salvage from cobinamide I, hexitol fermentation to lactate formate ethanol and acetate, purine nucleotides degradation II aerobic, L tryptophan biosynthesis and inosine 5 phosphate biosynthesis III pathway showed significant protection against KOA. (OR = 0.93,95%CI = 0.86–1.00;OR = 0.94,95%CI = 0.88–1.00;OR = 0.91,95%CI = 0.86–0.97;OR = 0.95,95%CI = 0.92–0.99; OR = 0.91, 95%CI = 0.85–0.98) Further multiplicity and sensitivity analyses demonstrated the robustness of the results. ConclusionOur study identified specific metabolic pathways in gut microbiota that promote or inhibit KOA, which provides the most substantial evidence-based medical evidence for the pathogenesis and prevention of KOA.