A numerical method to estimate temperature distribution during the cure of epoxy-terminated poly(phenylene ether ketone) (E-PEK)-based composite is suggested. The effect of the temperature distribution on the selection of cure cycle is evaluated using a suggested alternation criterion. The effect of varying heating rate and thickness on the temperature distribution, viscosity distribution and distribution of the extent of cure reaction are discussed based on the combination of the here-established temperature distribution model and the previously established curing kinetics model and chemorheological model. It is found that, for a thin composite (<=10mm) and low heating rate (<=2.5K/min), the effect of temperature distribution on cure cycle and on the processing window for pressure application can be neglected. Low heating rate is of benefit to reduce the temperature gradient. The processing window for pressure application becomes narrower with increasing thicknesses of composite sheets. The validity of the temperature distribution model and the modified processing window is evaluated through the characterization of mechanical and physical properties of E-PEK-based composite fabricated according to different temperature distribution conditions.