Abstract: Metabolic functional diversity of soil microorganisms can greatly contribute to the health of the soil ecosystems in facility vegetable field. However, the soil quality is seriously deteriorated in recent years, due to the frequency input of organic and chemical fertilizers, pesticides, and fungicides. The Biolog-Eco method has been widely used to demonstrate the carbon metabolic activity of culturable microorganisms. The ecological status of microbial communities can also be characterized by the metabolic functional diversity in diverse environments. In this study, a systematic investigation was carried out to clarify the impacts of cultivation periods and geographical location on the functional diversity of soil microbial metabolism using a Biolog-Eco microplate. Correlation analysis and Redundancy Analysis (RDA) were used to reveal the relative bacterial phyla and effect factors. The soil samples were collected from 11 facility vegetable fields in the two typical vegetable cultivation counties (Anqiu and Shouguang) of China. The key influencing factors were then identified for the microorganisms and carbon source utilization. The results showed that the Average Well Color Development (AWCD), Simpson index, McIntosh index, and Shannon index decreased with the increase of cultivation years, except for the AQ4 (cultivation history of 14 a in Anqiu), and SG4 (cultivation history of 10 a in Shouguang). The Principal Component Analysis (PCA) result demonstrated that the difference in the soil microbial utilization of carbon sources between two counties was much more significant than those among the soils with different cultivation histories in the same county. It infers that the geographical location played a more important role than the cultivation years. Correlation analysis showed that 16 different carbon sources (six types of carbon source involved) were closely related to the different bacterial phyla (P<0.05), and Firmicutes of soil bacterial phylum was positively related to the most kinds of carbon sources (9 kinds) in the Anqiu soil. In Shouguang soil, 11 different carbon sources (four types: carbohydrates, amino acids, carboxylic acids, and polymers) were closely related to the different bacterial phyla (P<0.05), and Latescibacteria positively related to most kinds of carbon sources (4 kinds). RDA showed that the Cd was the top environmental factor, negatively affecting the soil microbial carbon sources utilization in Anqiu soil (P<0.01), while the positive effect of organic matter was significant (P<0.01). Zn, organic matter, and Cd were negatively dominated the utilization of microbial carbon sources (P<0.05) in Shouguang, whereas, the effects of As and pH were significantly positive (P<0.05). This finding can provide direct evidence that the significant decrease in soil microbial functional diversity was caused by the long-term cultivation of facility vegetable, different relative bacteria and effect factors caused by location in the north of China. It is urgent to take different measures according to different situation to improve the soil micro-environment for the healthy environments in the vegetable fields.