Barnyardgrass (a monocotyledon) and yerbadetajo (a dicotyledon) are the most troublesome weeds in rice fields in China. The synthetic auxin herbicide florpyrauxifen-benzyl can effectively control both weeds. The objective of this research was to clarify modes of action of florpyrauxifen-benzyl in barnyardgrass and yerbadetajo. Our results showed that yerbadetajo was more sensitive to florpyrauxifen-benzyl than barnyardgrass: the 50% growth rate inhibition in barnyardgrass and yerbadetajo was 4.14 and 0.38 g a.i. ha−1, respectively. Florpyrauxifen-benzyl induced the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and abscisic acid (ABA) in yerbadetajo within 24 h, while in barnyardgrass, the highest production occurred at 12 h and decreased at 24 h. ACC and ABA levels in yerbadetajo at 24 h of treatment were significantly higher than those in barnyardgrass at any time. There were less differentially expressed genes related to ethylene and ABA synthesis in barnyardgrass than in yerbadetajo. There were five genes induced to increase by florpyrauxifen-benzyl in barnyardgrass and eleven genes in yerbadetajo. More ACC oxidase genes (ACO) were induced in barnyardgrass and more ACC synthesis genes (ACS) in yerbadetajo, especially three ACS3 (>30 fold). We speculated that differences in gene expression caused differences in ethylene and ABA production, leading to differences in phytotoxicity.