In the production of biofuel from lignocellulosic biomass, cost-effective pretreatment technologies play an important role in meeting the world's demand for bioenergy. In this study, Eichhornia crassipes (EC), sugarcane bagasse (SB) and Metasequoia glyptostroboides (MG) were pretreated by Fenton reagent (FT) and peroxyacetic acid (PAA), respectively, and then subjected to enzymatic saccharification. The optimal pretreatments for the three types of biomass were FT, PAA, and PAA, respectively. Overall, FT exhibited a higher ability to remove lignin from EC and increase the EC carbohydrate contents (from 67.48% to 86.57%), while PAA performed better in lignin removal from SB and MG, and increasing carbohydrate contents of SB (from 68.83% to 90.63%) and MG (from 71.96% to 93.73%). Furthermore, following their respective optimal pretreatments, the cell surfaces of each plant type were observably compromised, with distinct increases to the specific surface area, inner porosity, and enhanced substrate crystallinity, thus entailing significantly improved carbohydrate accessibility to enzymes. The results ultimately indicated that FT pretreatment was more appropriate for plant biomass with lower lignin content and lower crystallinity index (CrI), while PAA pretreatment was more suitable for plant biomass with higher lignin content and higher CrI. These findings will facilitate efforts to improve the feasibility of biomass-to-energy conversion.