Heavy metal pollution significantly reduces the quality of the environment and threatens human health especially in industrial cities. This study investigated toxic metals concentrations, pollution levels and human health risks assessment of urban soils in Yazd city, as an industrial city in center of Iran. Soil surface samples (0–10 cm) were collected from 30 points in the area for geochemical analysis. The concentrations of heavy metals were determined using an inductively coupled plasma mass spectrometry (ICP-MS).The values of the mean concentrations of toxic metals (mg kg− 1) in the urban soils decrease in the order of Zn (83.9) > Pb (34.5) > Cr (32.6) > Cu (23.5) > Ni (23.4) > As (5.86) > Co (4.86) > Cd (0.27). The mean concentration of Zn, Pb, As and Cd elements were higher than the background and the crust values. A pollution assessment by Geo-accumulation Index (Igeo), Pollution Index (PI), Contamination Degree (CD), the Integrated Pollution Index (IPI), the Pollution Load Index (PLI) and Integrated Nemerow Pollution Index (INPI) showed that As, Cd and Pb were moderately enriched and the study area polluted considerably by these toxic metals. Based on PI results, 88.9% of the urban soil samples highly polluted by As. Overall, the quality of the urban soil in Yazd city is clearly affected by toxic metals. Due to the prevailing wind direction, the route of the north-south highway of Iran and the population density and traffic of the northwestern and southern areas of the study area were found the highest level of pollution indicators (IPI > 1.8; LPI > 1.3; CD >15 and INPI > 4.3). The results of Pearson correlation analysis indicated that all pollution evaluation indicators were influenced by As and Cu, and showed high significant correlation with these two elements, while neither of them had a significant relationship with Pb and was found also a weak link statistically with Cd. Health Risk assessment of toxic metals has been performed in both carcinogenic and non-carcinogenic sectors. The results indicate that oral intake is the main pathway that toxic metals can harm human health for both the child and adults. The carcinogenic risks (RI) of adults and child by toxic metals were as follows: Ni > Pb > Cr > As > Cd. Hazard quotients (HQ) and hazard index (HI) values for child also were higher than these for adults. Generally, the results demonstrated that the potential carcinogenic health risks for adults of toxic metals was in an acceptable range in study area whereas for Cr, Ni and Pb with RI > 10− 4, the risk of cancer in child probably increase.