The invention relates to a method for identifying the number of effective parents in grass carp intraspecific cross combinations. The method includes the steps: 1) selecting parent fishes, marking theparent fishes and placing the parent fishes of different groups or strains needed for cross into the same parent pond in a first year to perform prenatal culture; 2) manually injecting hormone solution for acceleration of maturation in a second year, performing artificial fertilization to obtain fertilized ova, mixing the fertilized ova in the same combination and different families in a balancedmanner and placing the fertilized ova into the same circular hatching channel for hatching; 3) performing progeny test on the different combinations obtained in the step 2) by a paternity test method, determining the specific number of the effective parents in each combination offspring from cross parents and maintaining the combinations with more effective parents. The method has the advantagesthat molecular marker-assisted selection is combined with cross selection, maternal effects are decreased, cross parent contribution rate difference caused by different brood amount of the parents isdecreased, the number of the effective parents in each combination offspring is determined, and each combination can take cross advantages.