Abstract: Manganese is a kind of necessary trace element for the growth and development of rice. The author took rice seedlings as material, discussed the effect of manganese on the growth and physiological effect of rice seedlings. The author used water planting method, designed manganese deficiency and manganese excess treatments and measured agronomic traits and physiological and biochemical indexes of rice seedlings. The results showed that rice seedlings were sensitive to manganese stress. The plant height, root length, fresh weight, chlorophyll and soluble protein content decreased in different degrees, while MDA content increased, POD activity decreased; the extent of damage in rice seedlings was as follows: 1000 Mn>100 Mn>-Mn. Both manganese deficiency and excess could adversely affect the growth of rice seedlings, manganese should be reasonably applied.