Phthalate esters (PAEs) are ubiquitous in agricultural soil and crops because of the widespread application of plastic films containing PAEs. The enzymes play critical roles in the elimination of pollutants from environmental matrices. In an attempt to evaluate the effect of enzymes on the degradation of various PAEs, this study investigated the enzyme-catalyzed reaction kinetics of seven selected PAE congeners in water and soil. Carboxylesterase and lipase catalyzed the transformation of PAEs to monoalkyl phthalate esters and phthalic acid with the half-life ranges of 4.78–126.03 h. PAEs with long-alkyl-chain were more recalcitrant to carboxylesterase and lipase-catalyzed degradation, and PAEs with short alkyl chains were relatively easier to be degraded by the two enzymes. The results indicate that the alkyl chain length had a profound effect on the enzyme-catalyzed degradation of PAEs. The reaction rates and half-lives were significantly correlated with the logKow value (p < 0.01), which was dominated by the molecular structure. The results obtained in this work are expected to well guide the application of carboxylesterase and lipase in the remediation of waterbody contaminated by various PAEs. With respect to soil, they can be well used in the remediation, exposure, and risk assessment of paddy soil. However, the application of the results in the remediation of other soils might lead to the risk of a low removal ratio.