The comprehensive quality assessment of farmland soil is critical for agricultural production and soil ecological protection. Currently, there is no systematic method for conducting a comprehensive quality assessment of farmland soil; subsequently, as the most developed economic area in China, the comprehensive quality assessment of farmland soil in the Yangtze River Delta is lacking. We chose the farmland soil of Suzhou city as the research object. The soil fertility index (SFI) and soil environment index (SEI) were calculated with the membership function and Nemerow index. Finally, the comprehensive assessment of soil quality was achieved with the TOPSIS model. The results showed that the average values of soil pH, SOM, TN, AHN, AP, and AK were 6.44 (slightly acidic), 28.17 g/kg (medium), 1.63 g/kg (rich), 118.16 mg/kg (medium), 38.31 mg/kg (rich), and 160.63 mg/kg (rich), respectively. For the concentrations of heavy metals, including Cr, Ni, Cu, Zn, Cd, and Pb, in 122 soil samples, the percentages exceeding the background values of Jiangsu province were 5.74%, 8.20%, 8.20%, 10.66%, 86.07%, and 84.43%, respectively. Cd and Pb were the main heavy metal pollutants on farmlands. The soil samples with SFI values below the medium level (SFI < 0.6) accounted for 44.26%, and samples with SEI values below the medium level (SEI < 0.6) accounted for 13.12%. The values of the soil quality index (SQI) ranged from 0.171 to 0.996, with an average SQI value of 0.586 (very poor—V), and approximately half of the farmland soil quality in Suzhou city needed to be further improved. In a word, this study provides a theoretical basis and scientific support for the quality assessment and rational utilization of farmland soil.