Carbon (C), nitrogen (N), and phosphorus (P) stoichiometric ratios give valuable insight into ecosystem function. The purpose of the present study is to probe into the C, N, and P stoichiometric characteristics in various organs and their relationships with soil factors of the dominant deciduous conifer plant species ( Taxodium ascendens and Taxodium distichum) during afforestation in the riparian zone of Three Gorges Reservoir. The results showed only a small change in the concentration of C in different plant organs and soils. T. ascendens contained mean N and P concentrations of 7.63 and 1.54 g/kg in fine roots, 5.10 and 0.56 g/kg in stems, and 15.48 and 2.30 g/kg in leaves, respectively. Whereas T. distichum had a mean N and P concentration of 7.08 and 1.37 g/kg in fine roots, 4.84 and 0.59 g/kg in stems, and 16.89 and 2.23 g/kg in leaves. The N:P ratios in all organs were below 14, indicating that N may have inhibited tree growth. The fine roots P and N:P of T. distichum were weak plasticity and weak homeostasis, and those of T. ascendens were plasticity and weak plasticity. Their stems and leaves adhere to strict homeostasis. N concentrations were significantly positively related to P concentrations in every tissue (except the stems of T. ascendens), and C concentrations were significantly positively associated with P concentrations in the stems and leaves of T. ascendens and T. distichum ( p < 0.05). Likewise, soil P and fine root P were positively associated ( p < 0.01). This study contributes to the understanding of deciduous conifer plant stoichiometry. It demonstrates N, P, and N:P stoichiometric homeostasis in T. ascendens and T. distichum, which can withstand flooding and are suitable for vegetation restoration in the hydro-fluctuation zone.