Understanding the factors affecting the species richness of alien and native plant is a key issue for predicting the spread of alien species and protecting rare and endangered native species in nature reserves. To investigate the factors affecting alien and native species richness in temperate nature reserves of China, we used a database of 25 nature reserves in Shandong Province of northern China, and studied the relationship of alien and native plant species richness with climatic and anthropogenic factors, as well as area and elevation range. We found that most of the nature reserves in Shandong Province have been invaded by alien plant species. The distribution of alien and native species responds to the same climatic factors, and temperature and precipitation exert strong effects on both groups. Alien and native plant species richness are positively correlated. Human activity is more effective for explaining richness of alien than for native species. Simultaneously, human activity has stronger effects on alien herbaceous than on alien woody plants. Our results suggest that native species richness is mainly explained by climatic factors, whereas alien species richness is mainly explained by climatic factors and human activity together.