Sulfonated poly(ether ether ketone) (SPEEK) membrane with high sulfonation degree (SD) is a promising substitute of Nafion as proton exchange membrane (PEM), due to the excellent proton conductivity and low cost. However, its widespread application is limited by the inferior structural stability. Here, we report the fabrication of high SD SPEEK membrane with outstanding structural stability through an in-situ molecular-level hybridization method. Concretely, the ionic nanophase of SPEEK membrane is filled with precursors, which are then in-situ converted into polymer quantum dots (PQDs) by a microwave-assisted polycondensation process. In this manner, the micro-phase separation structure of SPEEK membrane is well maintained. PQDs with abundant hydrophilic functional groups together with the inherent –SO3H groups impart hybrid membrane highly enhanced proton conductivity of 138.2 mS cm−1 at 80 °C, which is comparable to Nafion. This then offers a 116.3% enhancement in device output power. Meanwhile, PQDs act as cross-linkers via generated electrostatic interactions with SPEEK, affording hybrid membrane with SD of 94.1% an ultralow swelling ratio of 1.35% at 25 °C, about 35 times lower than control membrane. More importantly, the in-situ molecular-level hybridization method is versatile, which can also boost the performances of chitosan (CS)-based membranes.