The ecological environment of semi-arid regions in China is fragile, and the situation of protecting environment is grim. So it is urgent to strengthen environment protection and ecological construction in semi-arid region. Four different vegetation ecosystems were selected in semi-arid region with Wuchuan County in Inner Mongolia as a case study: the bushes, the trees, the alfalfa land, and artificially mixed sowing grassland. The soil was sampled and carried to laboratory for analysis of the content of lead, cadmium and chromium in the soil in May and September (the start of the growing season and the end of the growing season). It was showed that among the four different ecosystems, the lead and cadmium contents in the soil were significantly different in variability, while the chromium is not significant. And the changing rate trend of the content of lead and cadmium is consistent: the contents of the both elements in May are higher than in September obviously. The degree of the order of the content change is also very close. The biggest of the change scope is from the bushes and artificially mixed sowing grassland, followed by the alfalfa land, and finally the trees. Therefore, it is more favorable to plant shrubs and grass for absorbing heavy metals in the soil in the common local vegetation eco-system.