Comparison of organic manure and conventional fertilizer were investigated in a simulated experiment with 20cm-, 40cm- and 60cm-high soil columns on nitrogen and phosphorus leaching and water pollution hazards from soil sampled from the watershed of the Fuxian Lake. Results showed that with the increase of irrigation frequency, TDN concentration in leaching water from organic manure increased gradually to the maximum and then decreased but it decreased continually from conventional fertilizer; the range of TDP concentrations in all the leaching water was narrow except in the leaching water from 20 cm soil column applied with conventional fertilizer. NO3--N and PO4-P were the main forms of nitrogen and phosphorus in the leaching water from different soil columns. The mean amount of total TDN and TDP leaching loss from conventional fertilizer were 157% and 52% of which from organic manure, respectively, which meant that groundwater pollution hazards of nitrogen due to conventional fertilizer leaching was higher than which due to organic manure, but on the contrary of groundwater pollution hazards of phosphorus.