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With the development of intensive aquaculture, worldwide concerns are increasingly focused on the biological control of farming wastes for the purpose of reducing nutrient loadings. In the present study, 5 experimental polyculture systems combining abalone and sea cucumber (SC) as different inter-species biomass ratios, i.e. 100:0, 70:30, 50:50, 30:70 and 0:100 (referred to as Group A, B, C, D and E, respectively), were set up to evaluate the potential of sea cucumber Apostichopus japonicus as scavengers to alleviate the farming wastes derived from the co-culture of abalone Haliotis discus hannai. Growth performance and significant isotopic shifts of the SCs in Groups B, C and D demonstrated the uptake of farming wastes, i.e. feces and uneaten feed residues. The proportional contributions of SC assimilated from uneaten feed residues, feces and sea mud were 21.7, 62.5 and 15.8% in Group B, 18.5, 54.3 and 27.2% in Group C, 11.5, 44.4 and 44.1% in Group D, respectively. The results revealed that sea cucumber had great potential to become an effective organic extractive species and aid in the concordant reduction of farming wastes in polyculture systems. The biomass ratio of abalone to sea cucumber 70:30 was recommended for aquaculture practice as providing the greatest economic and environmental benefits.