In this research, wheat, rice, and corn residue were used as a substrate for biogas production. Due to the high amount of lignin in all three substrates (> 9.9) and in order to increase the degradability of these substrates, an ultrasonic pretreatment with a power of 150 w at 15 min was used prior to initiating enzymatic digestion process. Some physical and chemical properties including solid and volatile particles and contents of lignin, cellulose and hemicellulose were measured before and after digesting the substances; and in addition, the biogas compounds including hydrogen, methane, hydrogen sulfide and carbon monoxide was measured during digestion. The metabolic pathways of converting glucose as the main constituent of all three waste types into biogas were studied to determine the factors affecting biogas compounds. The results showed that use of ultrasonic pretreatment in all three wastes increased the breakdown of lignin structures, which decreased the content of these structures in the feedstock compared to the substrate. The amount of solid and volatile particles of the feedstock obtained from the substrate of wheat residue was 35.1% and 95.3%, respectively, which was more than that of the other substrates. The highest amounts of reduction of solid particles (19.6%), volatile particles (18%), cellulose (12.6%), hemicellulose (4.4%) and lignin (3.6%) were related to the feedstock obtained from wheat residue. Analyses of biogas compounds showed that the highest biohydrogen production obtained for wheat substrate (ppm 18000), but its biomethane production was lower than the other substrates. The highest amounts of biohydrogen production of all the substrates occurred after seven days, which was related to the butyrate acidification stage. With increasing digestion time, hydrogen production decreased while the other biogas compounds increased. One of the probable reasons was the consumption of hydrogen produced in the stages of hydrolysis, acidification and acetate formation in the stages of alcoholization and methanation. The highest amount of hydrogen production was related to the stage of butyrate formation and then acetate formation. The higher production of biohydrogen by wheat residue is most likely due to its high volume of volatile, hydrocarbon and hemicellulose compounds. While the low production of hydrogen by corn residue was due to driving the reactions towards the production of ethanol and consuming hydrogen.