Co-fermentation of carbon-rich and nitrogen-rich feedstocks with suitable carbon to nitrogen (C/N) ratios is commonly considered as a viable way to enhance biological hydrogen production. In this study, cassava residue (C/N ratio = 29.1) and swine manure (C/N ratio = 8.6) were mixed and subject to microwave-assisted acid hydrothermal pretreatment. The resulting hydrolysates were used for subsequent dark hydrogen fermentation. However, the mixture with a C/N ratio of 15.1 resulted in the lowest hydrogen yield potential of 107.8 mL/g volatile solid (VS). Comparatively, the mono-fermentation of cassava residue exhibited the highest hydrogen yield potential of 145.6 mL/g VS and a peak hydrogen production rate of 8.2 mL/g VS/h. The modified Gompertz model was employed for kinetic analysis, and suggested that the lag-phase time and peak time of hydrogen fermentation exhibited a significantly positive linear correlation with increased C/N ratios. Reducing sugars analysis indicated that pretreatment of mixed cassava residue and swine manure led to a decrease of total sugar yield by 7.2-10.5% due to the Maillard reactions between hydrolyzed sugars and amino acids. A reaction mechanism based on glucose and arginine was proposed to elucidate the Maillard interactions between carbonyl group (-C=O) and amino group (-NH2), which was responsible for the overall sugar loss. The findings of this study suggested that pretreatment for mixed carbohydrate-rich and protein-rich feedstocks needs to be optimised to avoid unexpected fermentable sugars loss.