In order to explore the fertilizer effect of biogas fertilizer (BF) in vegetable planting, three rounds of Shanghai cabbage-eggplant rotation planting experiments were carried out in the greenhouse, and the application rates of low (BF-L), medium (BF-M) and high (BF-H) biogas fertilizer were set up. The effect of BF replacing chemical fertilizer (CF) and the threshold value of highload land consumption of BF were discussed from the perspectives of yield, soil characteristics and heavy metal risk. The results showed that the yield of BF groups was 6% lower than that of CF group in Shanghai cabbage planting, and the average yield of BF-M group was the highest in BF groups (39.7t/hm2). In eggplant planting, the yield of BF groups was higher than that of CF group, and the average yield of BF-H group was the highest, reaching 58.3t/hm2, which was 27% higher than that of CF group. After two years of continuous application of BF, the total nitrogen (TN) and total phosphorus (TP) contents of soil were increased significantly, and the increase was much higher than that of CF group. The TN content of soil in BF-M and BF-H groups was increased by 84% and 85% compared with that of the original soil, and the TP content of soil was increased by 3.4 times and 3.2 times. However, the effect of BF application on soil total potassium (TK) content was not obvious, which was only about 17% higher than that of the original soil. In addition, the soil pH value of continuous application of BF was more stable, which can effectively alleviate the problem of soil acidification caused by nitrogen fertilizer application. However, like CF, BF application had a greater impact on soil electric conductivity (EC). The soil EC value of BF-M and BF-H groups showed an increasing trend year by year, with an increase of more than 70% compared with that of the original soil. Furthermore, there was no risk of excessive heavy metals and heavy metal intake in the three seasons of vegetables harvested, and there was no phenomenon that the heavy metal content of vegetables increased year by year. Moreover, the continuous application of BF only caused the accumulation of Cu and Zn in soil, but it was still within the standard limit, and had no significant effect on the content of Pb, Cr, Cd, As and Hg in soil, and there was no heavy metal pollution caused by BF application. The research result can provide a reference for the evaluation of fertilizer efficiency and safety of continuous rounds of high-load BF application in facility vegetable cultivation.