The mathematical model of optimal water quantity allocation for a single main canal in a large-scale irrigation area was constructed that took the minimal sum of the squared deviation of water shortage for water receiving areas controlled by the single main canal in one given irrigation period as the study target, and the total irrigation quantity of the single main canal as a constraint condition. Taking the optimal allocation of water quantity of each branch canal as decision variables, and several branch canals under the irrigation sequence of the main canal as a state variable, this model was solved by the one-dimensional dynamic programming (DP) method, by which the minimal water shortage and corresponding optimal water quantity allocation of each branch canal was calculated. The proposed method could provide a decision-making reference for optimal water resources allocation of single main canal irrigation areas, and also provide the theoretical basis for optimal water quantity allocation of a main canal with rotation irrigation by strips or with segmented rotation irrigation mode in China’s large-scale irrigation areas. Taking Hengliu Main Canal of Zhouqiao Irrigation Area in Jiangsu Province as a study case, optimization results showed that in a medium drought year (p = 75%) and a special drought year (p = 95%), minimal water shortage for water receiving areas controlled by Hengliu Main Canal was respectively 2.57 × 104 m3 and 23.31 × 104 m3 during the ponding period of rice. The corresponding water quantity allocation for each branch canal has reflected a compellent model solution precision and efficiency.