Beckmannia syzigachne is a noxious grassy weed that infests wheat fields in China. Previously, we identified that mesosulfuron-methyl resistance in a B. syzigachne population (R, SD04) was conferred by non-target resistance, such as cytochrome P450 mixed-function oxidases (P450s)-based metabolism. RNA sequencing and real-time PCR (qRT-PCR) were used to discover potential P450s-resistant-related genes. Five cytochrome P450s (CYP704A177, CYP96B84, CYP71D7, CYP93A1, and CYP99A44) were found to be highly expressed in R plants. In this study, CYP99A44 and CYP704A177 were cloned from B. syzigachne and transferred into Arabidopsis thaliana to test the sensitivity of Arabidopsis with and without P450s genes to mesosulfuron-methyl and other acetolactate synthase (ALS)-inhibiting herbicides. Transgenic Arabidopsis overexpressing CYP99A44 became resistant to the sulfonylurea herbicide mesosulfuron-methyl, but showed no resistance to pyroxsulam, imazethapyr, flucarbazone, and bispyribac-sodium. Notably, those overexpressing CYP704A177 showed resistance to pyroxsulam and bispyribac-sodium, but not to mesosulfuron-methyl, imazethapyr, and flucarbazone. These results indicated that B. syzigachne and transgenic Arabidopsis displayed different cross-resistance patterns to ALS-inhibiting herbicides. Subcellular localization revealed that CYP99A44 and CYP704A177 protein were located in the endoplasmic reticulum. Furthermore, these results clearly indicated that CYP99A44-mediated mesosulfuron-methyl resistance in B. syzigachne and CYP704A177 may be involved in B. syzigachne cross-resistance to pyroxsulam and bispyribac-sodium.