Microscale parts made of Polyether-Ether-Ketone (PEEK) are widely used in biomedical, aerospace, and manufacturing industries. The formation mechanism of the chip and machining quality of PEEK are closely related during the micromilling process. However, they have not been sufficiently studied yet. Therefore, the chip shape during the micromilling process is investigated in this research to gain an in-depth understanding of the micromilling process of PEEK. Firstly, a finite-element simulation model is constructed and used to investigate the relationships of feed speed in relation to strain rate and chip shape. Secondly, the chip shape is classified from the experimental results and process intervals are explored corresponding to each kind of chip shape. Then, the relationships between the chip shape and evaluation indexes (milling force F, maximum cutting temperature Tmax, surface roughness Ra) are investigated. It turns out that four main types of chip shapes are produced during the micromilling process of PEEK, namely, the flake chip, the ribbon chip, the curl chip, and the broken chip. Different kinds of chip shapes can be obtained by controlling the process parameters during the micromilling process. The stability of the cutting process can be judged and the machining quality can be initially discerned based on the chip shapes.