Two rice varieties with varied perchlorate-sensitivity were selected to study their response when exposed to perchlorate-contaminated environment. Gannuoxiang is a perchlorate-resistance rice variety while IR65598-112-2 is a perchlorate-sensitive rice variety. A pot experiment was conducted to study the effects of perchlorate stress on plant growth, development and nutrient uptake. Perchlorate with three concentration levels at 0.2, 2.0 and 4.0 mmol/kg was added to the soil for different treatments at the end of recovering stage after transplanting. Results showed that (1) the higher the concentration of perchlorate in soil, the higher the rate of growth inhibition of the two rice varieties. The symptom of the perchlorate effect on rice was more and more obvious as time went on. The rates of the growth inhibition were 3.08%, 33.39%, 39.03% to Gannuoxiang and 9.18%, 21.07%, 34.97% to IR65598-112-2 under the three concentration levels of perchlorate in the tillering stage of rice. (2) The rice tiller number of all treatments except Gannuoxiang at 0.2 mmol/kg level decreased significantly. (3) All perchlorate treatments delayed heading and maturity. The delay reached about one month under high level perchlorate treatment. (4) IR65598-112-2 showed earlier respond to perchlorate and more sensitive to low concentration of perchlorate than Gannuoxiang. (5) The phytotoxic effect of perchlorate on rice root was more serious than on its aboveground parts. (6) Perchlorate pollution significantly decreased the biomass of rice. The accumulation of total nitrogen and total phosphorus was reduced markedly. In conclusion, perchlorate pollution can decrease the growth and tiller number of the two rice varieties, delay their development, consequently, result in low biomass and low accumulation of nutrient. The phyto-toxicity of perchlorate to rice not only depended on the pollutant concentration and its duration, but also on the specific rice varieties and its organs.