By the combination of serial selective extraction, with diethylene glycol distearate (DGD) embedment and embedment-free electron microscopy, as well as SDS-PAGE，the intermediate filament (IF) matrix system, which is composed of the filament about 10 nm in diameter and filament band，was observed in vegetative cells and resting cysts of Euplotes encysticus. In vegetative cells，a three dimensions scaffold formed by IF occupies the whole epiplasm with denser filament network beneath the pellicle. The filament of cytoplasm deeps beneath the epiplasm makes up of a looser network attached by organelle and some dense electronic granules. The LA was a laminar structure, which was composed of parallel filaments. The nuclear matrix filament network distributes more intensively and no dense electronic granules attached. The similar more compact network is also seen in the resting cyst, which may be caused by the widely contraction in the course of encystment in infusorians. Remarkably, the filament network is also observed in the innercystwall of resting cyst, and its filament network distributes equably and densely in the whole cyst wall. SDSPAGE shows that only parts of the proteins have preserved when the cyst is formed, part lost, and some distinct proteins have produced.Conclusions: the intermediate filamentlaminanuclear matrix system is a stable structure in both vegetative and resting cyst, and it may play a more important role than the microtubule matrix. Besides the special cingulums in this system of cyst may be the important proteins needed in resting cyst.