Soil security plays an important role in the sustainable agriculture. With the rapid economic development, the soil quality faces great human-related threats from the contamination, and it is essential to conduct the investigation of heavy metals in soils of the areas with intensive human activities. Source apportionment and spatial prediction are the key issues of the investigation of soil heavy metals pollution, which could provide scientific references for the regional soil pollution management and remediation. For this purpose, a total of 1067 samples were collected in surface soils of Yantai coastal zone, eastern China; and As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, and Zn concentrations were analyzed. Positive matrix factorization (PMF) was applied to estimate source apportionment of heavy metals. Multivariate independent simulation combining Independent Component Analysis (ICA) and Sequential Gaussian Simulation (SGS) were proposed to predict the spatial distributions of heavy metals, and local and spatial uncertainty analysis was used to identify the polluted areas. As, Co, Cr, Mn, and Ni originated from natural sources, with their spatial distributions consistent with parent materials. Cd, Cu, Hg, Pb, and Zn exhibited significant accumulation in soils, but the mean contents of these five heavy metals did not exceed the risk screening values for soil contamination of agricultural land. Industrial and traffic emissions contributed 58.3%, 40.3%, and 35.8% of Cd, Pb, and Zn concentrations, respectively; and these three heavy metals presented high values in gold and copper tailings as well as the urban district of Yantai. Cu mainly came from the application of bordeaux mixture and organic fertilizer, with its high-value hotspots associated with orchard soils. Hg originated from the atmosphere deposition originated from coal combustion and gold smelting by the mixed mercury method, and its high-value hotspots were related to the surrounding of gold mine as well as urban areas of Longkou and Penglai. The potential contaminated areas of Cu, Hg, and Cd accounted for 37.5%, 14.3%, and 8.6% of the total study area, respectively.