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A compare study is performed on field effect phototransistors (FEpT) with two typical heterojunctions based on graphene and PbSe quantum dots (QDs) hybrid, including layer-heterojunction (LH) and bulk-heterojunction (BH). LH-FEpT exhibits a higher mobility ({\\mu}n) 677 cm2V-1s-1, whereas {\\mu}n of BH-FEpT is as low as 314 cm2V-1s-1, however the higher responsivity (106 A/W) is achieved by the former. 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