The invention discloses a crop seedling stage drought resistance identification method employing bottom upward percolation re-watering technology. The method comprises following steps: (1) preparing materials; (2) manufacturing water tanks; (3) adding soil into boxes; (4) combing the sowing boxes and the water tanks; (5) sowing seeds; (6) re-watering the seeds; and (7) draining the water. The beneficial effects of the method are that the crop seedling stage drought resistance identification method employs the bottom upward percolation re-watering technology, so that seedling stage drought resistance identification on crops having different germplasms can be performed on a large scale, and the identification is easy; the crops can be simultaneously re-watered in batch through the bottom upward percolation re-watering technology, the influence caused by different watering time in the same repeating process is avoided, and the working efficiency is improved; a problem that heat shock effects on the crops may be easily formed through a soil surface watering manner under a high-temperature and high light intensity condition is overcome; a soil hardening phenomenon is avoided; the physiological metabolism and growth of roots are not influenced; the water content between the sowing boxes and in the sowing boxes are the same; and the accuracy of a test is greatly improved.