Aiming to improve safety and stability in manufacturing poly-ether-ether-ketone (PEEK) prepreg by powder impregnation, the aqueous system combined with surfactant and thickener was proposed in this paper. Based on surface tension method, the effects of surfactants and concentration on dispersion efficiency of PEEK powders were studied, and concentration of surfactants was determined. The effect of thickener concentration on suspension stability was analyzed, and ingredients of aqueous system were optimized by mechanical tests. The results show that, dispersion efficiency would reach maximum when surfactant concentration at critical micelle concentration, but not affected by the type of surfactant. Network association mechanism of thickener could improve stability of suspension, which holding time was increased from 40 min to 4 h. The good dispersion effect and long times stable system improved the coefficient variation of resin mass fraction, which was reduced from 7% to 4%. Compared with circulating system, the mechanical test results showed that the tensile strength kept unchanged, but interlayer properties were associated with carbon residue mass, the lower the residue carbon mass, the higher the interlayer strength retention rate, the optimized ingredient was Aerosol OT 75%E solution. Aqueous system has characteristics of safety, green, and low cost, which fits the demands of industrial production of prepreg.