This study investigated the physiological metabolites content of tomato seedlings by different grafting treatment. The result shows that the metabolites of tomato seedlings were affected by grafting treatment. The content of chlorophyll, protein, proline, total soluble carbohydrate, and malondialdehyde in leaves were analyzed for 8days after grafting treatment, and they changed evidently. The contents of proline and total soluble carbohydrate content were significantly different not only between grafted and self rooted tomato seedlings, but also between fully matched grafts and half matched grafts, therefore, the proline and total soluble carbohydrate content of tomato seedling would be good physiological indicators for grafting treatment, and can be the reference for studies concerning tomato grafting and enhancing the qualities of the seedlings.