Integrated rice-duck farming system, developed from “raising ducks in paddy fields”, as one of China’s traditional agriculture was encouraged for safe production of rice in China, Japan and other countries in Southeast Asia. To study the effects of ducks on the growth characteristics of rice, a mechanical stimulation experiment was conducted under greenhouse conditions. Based on the analysis, mechanical stimulation showed some impacts of raising ducks on the agronomic characteristics of rice. Different intensities of mechanical stimulation restrained and decreased total rice height by 8~10 cm at harvest stage. The lengths of different sections of rice stem, especially the length of the above-ground second section, reduced under duck-rice farming. The thickness of rice stem increased under enhanced mechanical stimulation, with the highest increment of 0.17 cm after 40 days of treatment. While mechanical stimulation for a certain period improved effective tillering capacity of rice, it obviously decreased shoot biomass by about 19.6% after 40 days of treatment, which led to an increase in root/shoot ratio. Moreover, mechanical stimulation changed some characteristics of rice yield formation. Under enhanced stimulation intensity, average length of rice ear increased by 8.88%. Also empty grain number per rice ear decreased by about 36.12%. Rice seed setting rate was higher by 3.79% under increased mechanical stimulation than the control. These findings further verified the effects of mechanical stimulation on plant growth, providing the basic scientific references for the improvement and reasonable utilization of duck-rice integrated farming system.