To accurately assess the potential ecological risk posed by heavy metals in lime concretion black soil and quantify the risk contributions from different sources, an investigation of 217 surface soil samples and 56 subsoil samples was performed in the southern part of Suzhou City. Geochemical baseline values of soil heavy metals (Cr, Zn, Pb, Ni, Hg, Cu, Cd, As, Mn and Co) in the study area were calculated as 53.6, 61.5, 19.8, 27.6, 0.08, 18.4, 0.13, 12.9, 416.1 and 11.0 mg/kg, respectively, by using reference metal normalization and cumulative frequency curve methods. Subsequently, four potential sources of soil heavy metals were identified by the positive matrix factorization. Finally, the potential ecological risks arising from the identified sources were determined by the integrated model of positive matrix factorization and Hakanson potential ecological risk index. Results showed that the ecological risk posed by soil heavy metals in the study area ranged from low to moderate level. Hg and Cd were the two largest risk contributors, supplying 36.0% and 30.3% of total risk value. The origin of heavy metals in the soils is mostly related to four sources including agricultural activities, natural dispersion, coal consumption and traffic pollution. Source apportionment of the potential ecological risks revealed that the dominant risk source in the study area was natural dispersion (42.0%), followed by coal related industries (26.5%), agricultural activities (20.4%) and traffic pollution (11.1%). This work gives a clear baseline information of the heavy metal accumulations in lime concretion black soil and provides a successful case study for the source-oriented ecological risk assessment.