A hand-held pneumatic pollinator for hybrid rice seed production and a method thereof are provided. The pollinator includes a hand-held power chassis, a lifting assembly, a pneumatic pollination assembly, and a control assembly. A position of each of air blowing pipes relative to an ear of the male parent is adjusted by the control assembly and the lifting assembly. The pneumatic pollination assembly is provided with a plurality of air blowing pipes, of which the number is less than rows of the male parent of a hybrid rice seed production with a relatively large row ratio. Each air blowing pipe is located between corresponding two rows of the male parent during pollination. The directional, uniform and constant airflow at an air blowing port blows a pollen off a stamen to transport the pollen to the female parent compartment.