Peat moss as a kind of optical substrate is widely used in horticultural industry, it will be harmful to environment if peat moss is be unrestrained exploited. Exploring alternative substrate with stable performance becomes a hot spot of scientific research at home and abroad. In this experiment, the corn stalk substrate mixed with vermiculite in definite proportion was used for tomato seedling culture and was compared with peat moss. The corn stalk substrate was soaked in water in different time with the volume radio of 1:2 corn stalk substrate to water the soaked substrates would be air dried before using for growing tomato seedling. The effects of corn stalk substrate soaking in water in different time on the seedling growth were studied by measuring the coefficients of aboveground and underground parts growth and dry matter quantities regularly during the tomato seedling growing stage. The results indicated that the water-soaked corn stalk substrate could accelerated the tomato seedling growth and increased aboveground, underground parts growth and whole plant fresh and dry matter weight, the longer the tomato seedling growth, the more obviously the effects of these were. It was different that the effects of different soaking time in water on tomato seedling growth, prolonging soaking time properly could promote tomato growth and seedling dry matter accumulation, but these effects would be decreased with overtime soaking. The corn stalk substrate soaked in water in 10 d was an optimal treatment and could alternative peat moss in growing tomato seedling. It was an effective method for modified physicochemical properties of corn stalk substrate by soaked in water in some time.