Poly(ether ether ketone) (PEEK) hollow fiber membranes were successfully prepared from miscible blends of PEEK and polyetherimide (PEI) via thermally-induced phase separation (TIPS) with subsequent extraction of the PEI diluent. The phase structure evolution, extraction kinetics, membrane morphology, pore size distribution and permeability for the hollow fiber membrane were studied in detail. Extraction experiments, differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMA) studies showed that the heat treatment had a significant influence on the two-phase structure of PEEK/PEI, and that it was controlled by the crystallization kinetic of PEEK and the diffusion kinetic of PEI. As the annealing temperature increased, the controlling factor of the phase separation changed from PEEK crystallization to PEI diffusion, and the main distribution of the amorphous PEI chains were changed from the interlamellar region to the interfibrillar or interspherulitic regions of PEEK crystallization. When the annealing temperature increased from 240 °C to 280 °C, the extracted amount of PEI increased from 85.19 to 96.24 wt %, and the pore diameter of PEEK membrane increased from 10.59 to 37.85 nm, while the surface area of the PEEK membrane decreased from 111.9 to 83.69 m²/g. Moreover, the water flux of the PEEK hollow fiber membranes increased from 1.91 × 10⁻² to 1.65 × 10⁻¹ L h⁻¹ m⁻² bar⁻¹ as the annealing temperature increased from 240 °C to 270 °C. The structure and properties of the PEEK hollow fiber membrane can be effectively controlled by regulating heat treatment conditions.