Abstract: In order to select suitable floating system substrate for pepper, the germination characteristics and seedling growth indexes of pepper under three different substrates were studied. The results showed that the effects of different substrates on seed germination indexes were different significantly. The germination rate, germination potential, germination index and germination days of three varieties on substrate No. 2 were obviously higher than those of substrate No. 1 and substrate No. 3. On substrate No. 2, the germination rate, germination potential, germination index and germination days of sweet pepper were 89%, 53%, 43.23, 8.76, respectively, and 81%, 48%, 40.22, 10.86 for Kayan pepper, 86%, 50%, 42.67, 11.27 for giant pepper. In the period of four sampling, only on the 20th day the plant height, biomass, chlorophyll SPAD value and nitrogen, phosphorus, potassium content of substrate No. 2 significantly were higer than those of substrate No. 1 and substrate No. 3, and the differences were not obvious between three substrates in the 30th, 40th, 50th day. In summary, substrate No. 2 is more suitable for pepper floating seedling.