Phototransistors based on graphene–quantum dot hybrids have a high responsivity and gain. However, the influence of the type of heterojunction on the photoresponse of the transistors is still undetermined. A comparison was performed on field-effect phototransistors (FEpTs) with two types of heterojunctions: layered heterojunctions (LHs) and bulk heterojunctions (BHs). Through a comparative study, it was shown that BH–FEpTs had electron and hole mobilities (μE and μH) of 677 and 527 cm2 V−1 s−1 whereas LH–FEpTs had lower mobilities of μE = 314 cm2 V−1 s−1 and μH = 367 cm2 V−1 s−1. The large interfacial area in the BHs reduced the degree of channel order (α) by two orders of magnitude compared with the LHs. Although a higher mobility was achieved, an increase in the degree of channel disorder and the lack of an effective transfer mechanism limits the responsivity in BH–FEpTs. Therefore, LH–FEpTs are more appropriate candidates for near infrared phototransistors.