In this paper, the effects of annealing treatment on the microstructure, thermal property and magnetic properties of mechanical alloyed FeSiBAlNiC and FeSiBAlNiCe amorphous high entropy alloys has been systematically investigated using X-ray diffraction, differential scanning calorimetry, field emission scanning electron microscopy and alternation gradient magnetometry. The results showed that annealing at different temperature range induced the pronounced microstructural evolution from the amorphous phase to a mixture of amorphous phase and intermetallics but without any formation of solid solutions. In addition, the thermal stability and heat resistance were enhanced with increasing the annealing temperature. Similarly, annealing treatment also had significant effect on the particle morphology, making the particles evolve from near-round shape to plate-like shape. Furthermore, subsequent annealing of W6-Ce amorphous HEAs enhanced the saturation magnetization (Ms) remarkably (from 0.6 emu/g of 140 h as-milled W6-Ce to 20.17 emu/g). But for the Ms values of the 140 h as-milled amorphous W6-C HEAs, annealing in different temperature range all exhibited a slightly decreased effect.