Abstract: In order to reveal the effects of puddling methods on the morphology and physiological activity of rice root relative to yield formation in a paddy field in the cold region, a rice cultivar, Longjing 31 was used and three puddling methods were compared, i.e. dry flatting but no puddling (HP), wet flatting but no puddling (SP) and conventional puddling as the control (CK). The root morphology, root physiological activity, biomass and yield of rice at different growth stages were measured. The results showed that the root morphology tended to be stable at heading and flowering stages. Compared with CK, HP significantly increased total root length, total root surface area, total root volume and average root diameter by 14.1%, 8.79%, 7.16% and 4.06%, respectively, while SP only increased total root length by 6.43%. The physiological activity of root reached the maximum at the heading and flowering stages. Compared with CK, HP and SP significantly increased root oxidation activity by 16.1% and 5.51%, and root bleeding intensity by 10.2% and 5.74%, respectively. Compared with CK, the rice yield under HP and SP significantly increased by 7.65% and 4.03%. To sum up, compared with CK, HP can significantly improve root morphology and physiological activity, and then stimulate the aboveground growth and yield of rice.