The layer system of 48 targets was studied by using R-cluster analysis methods with fishery resource data (investigated from 1980 to 1992) of 55 reservoirs of 20 provinces in China. After comparing with the results of the two analysis methods, the target layer system for the fishery trophic classification of reservoirs in China was established. The 48 targets could be divided into 3 layers. The first layer includes 6 sub-levels: geography level (latitude-LN, illumination hours-IH), climatology level (annual no frost days-NFD, annual mean air temperature-AT, annual rainfall-RF), water depth level (maximum depth-MAXD, mean depth-MD), area and volume level (fishery area-FA, total storage capacity-TSC, profit storage capacity-PSC, dead storage capacity-DSC), soil level (catchment area-CA, draw-down area-DDA, DDA to FA index-DFI) and hydrology level (ratio of water exchange-RWE, CA to FA index-CFI, CA to TSC index-CCI).The second layer includes 5 sub-levels: major ions level, electrical conductivity-EC, total alkalinity-TA, total hardness-TH, value of pH-PH, TA to TH index-AHI), phosphorus level (phosphate phosphorus-P0_4-P, total phosphorus-TP), organic matter level (chemical oxygen demand-COD), dissolved gas level (dissolved oxygen-DO) and nitrogen level (ammonium nitrogen-NH_4-N, nitrite nitrogen-N0₂-N, nitrogen level nitrogen-N3, total nitrogen-TN).The third layer includes 4 sub-levels: phytoplankton level (density-DP, biomass-BP), zooplankton level (density-DZ, biomass-BZ), primary productivity level (phytoplankton primary productivity-PP), fish growth level (body length-SL and weight-SW and fatness-SFAT of two years silver carp, body length-BL and weight-BW and fatness-BFAT of two years bighead carp).