ABSTRACT Although application of calcium polyamino acid (Ca-polyAA) is one of the effective ways to improve saline-alkali soil and promote plant growth, the clear mechanisms are unknown. A two-year field experiment with four Ca-polyAA application treatments (added at rates of 0, 7.5, 15.0, and 22.5 × 103 kg ha−1) was conducted on saline-alkali soil in Songnen Plain of China. In the first year (2016), Ca-polyAA increased soil porosity and decreased pH, electrical conductivity (EC1:5) and exchangeable sodium percentage (ESP). Root Na+/K+ and Na+/Ca2+ ratio were reduced whereas hydraulic conductivity was increased. The hormone concentration and enzyme activity in the root were enhanced at tillering stage. Root structure development at the root tip was promoted after the application of Ca-polyAA. The total root length, surface area, volume and biomass were increased by increasing Ca-polyAA added rate. Similar results were obtained in the second year (2017). Path analysis demonstrate that Ca-polyAA can promote the accumulation of root biomass mainly by decreasing Na+/ K+ ratio, increasing root hydraulic conductivity and the activity of carbon metabolism enzymes, and the development of the root cortex. These results revealed that Ca-polyAA, as an efficient ameliorator, is capable to enhance agronomical and morphophysiological traits of rice in saline-alkali soil.