This study investigated the possible protective effect of combined fungal polysaccharides (CFP), consisting of Cordyceps sinensis polysaccharides (CSP) and Ganoderma atrum polysaccharides (PSG) with well-defined structural characteristics, against cyclophosphamide (CTX)-induced hepatotoxicity in mice. Our results indicated CFP effectively prevented the liver injury by decreasing toxicity markers (aspartate transaminase, alanine aminotransferase and alkaline phosphatase). Further biochemical and molecular analysis indicated CSP particularly inhibited the activation of Toll-like receptor 9 (TLR9) and its related inflammatory signals, including pro-inflammatory cytokines, inducible nitric oxide synthase, and cyclooxygenase-2 to modulate hepatic inflammation response. Relatively, through activation of peroxisome proliferator-activated receptor α (PPARα), PSG increased hepatic glutathione peroxidase and glutathione content depleted by CTX, as well as prevented mitochondria-dependent apoptosis with regulation on Bcl-2 family proteins (Bad, Bax and Bcl-2). In addition, protective effect of CFP was associated with enhanced modulations on cellular oxidant/antioxidant imbalance, mitochondrial apoptotic pathway and pro-inflammatory factors via PPARα upregulation and TLR9 downregulation. Taking together, the combinatorial approach based on CSP and PSG presented a practical option for the management of drug-induced liver injury.