Abstract: Filamentous fungus Sr18 is a documented bio-control fungus against nematodes with broad-spectrum nematocidal activity. In present research, high resolution field emission scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were used to observe the micro-structure surface as well as internal cellular ultrastructure of Bursaphelenchus xylophilus. The results of SEM indicated that small molecular active products damaged the B. xylophilus' heads, body wall and tail. The dissolved substance inside the cell flowed out was observed by SEM. The results of TEM indicated that nematodes' cuticle and coelom were separated, and cell nucleus were seriously damaged, and became irregular. The ribosomes on rough endoplasmic reticulum became aggregated. The mitochondria appeared vacuolated. The muscle cells were also damaged. The above phenomena demonstrated that the nematocidal mechanism of small molecular active products was poisoned holistically rather than surface contact action. The research provides scientific evidence for further revealing the nematocidal mechanism of Sr18 as well as the development of biological pesticide controlling nematodes.