Micron size particles of poly(ether ether ketone) (PEEK) were prepared by self-made pan-type milling equipment operated at ambient temperature. The changes of particle morphology, crystalline properties, thermal behavior, and viscosity-average molecular mass during milling were studied by SEM, WAXD, DSC, TGA, and viscosimetry analyses, respectively. SEM analysis indicated that pan-milling firstly destroyed the original structure of PEEK through squeezing in-between mill pans, then to produce fine powder undergoing the processes of deforming and size reduction. The average particle size of PEEK was reduced to 100 pm only after 5 cycles of pan-milling and reached less than 50 km after 50 cycles. DSC analysis showed that crystallinity of PEEK decreased with the pan-milling cycles, agreed with WAXD data. The crystallinity of PEEK decreased from 46.2 to 39.9% of 50 pan-milling cycles was offered. The glass transition temperature increased slightly along with pan-milling cycles. Mechanochemical effects caused by pan-milling were also studied. Viscometer test exhibited that molecular weight dropped quickly at earlier pan-milling stage then decreased slightly during later pan-milling. Pan-milling technique is an efficient, clean, and environmental friendly method for preparing fine PEEK powder.