Nitrogen-doped graphene quantum dots (N-GQDs) were decorated on a three-dimensional (3D) MoS2-reduced graphene oxide (rGO) framework via a facile hydrothermal method. The distribution of N-GQDs on the 3D MoS2-rGO framework was confirmed using X-ray photoelectron spectroscopy, energy dispersive X-ray elemental mapping, and high-resolution transmission electron microscopy techniques. The resultant 3D nanohybrid was successfully demonstrated as an efficient electrocatalyst toward the oxygen reduction reaction (ORR) under alkaline conditions. The chemical interaction between the electroactive N-GQDs and MoS2-rGO and the increased surface area and pore size of the N-GQDs/MoS2-rGO nanohybrid synergistically improved the ORR onset potential to +0.81 V vs reversible hydrogen electrode (RHE). Moreover, the N-GQDs/MoS2-rGO nanohybrid showed better ORR stability for up to 3000 cycles with negligible deviation in the half-wave potential (E 1/2). Most importantly, the N-GQDs/MoS2-rGO nanohybrid exhibited a superior methanol tolerance ability even under a high concentration of methanol (3.0 M) in alkaline medium. Hence, the development of a low-cost metal-free graphene quantum dot-based 3D nanohybrid with high methanol tolerance may open up a novel strategy to design selective cathode electrocatalysts for direct methanol fuel cell applications.