In order to explore the pollution level and source of soil heavy metals in Haikou City, taking the agricultural land in Haikou City as the research object, the content of eight kinds of heavy metals such as Cd, Hg, As, Pb, Cr, Cu, Ni and Zn in soil surface samples were collected and determined, and the spatial distribution characteristics of heavy metals were clarified combined with geostatistical analysis method. The single factor pollution index method, geo-accumulation index method and potential ecological risk index method were used to evaluate soil pollution. The source of heavy metals was quantitatively analyzed by the correlation analysis and principal component analysis/absolute principal component fraction (PCA/APCS) receptor model. Six heavy metals such as Cd, Pb, Cr, Cu, Ni and Zn exceeded the risk screening value of agricultural land, and the proportion of exceeding the standard points from high to low was Cr, Ni (31.6%)>Cu (21.1%)>Cd (5.3%)>Pb and Zn (2.6%). The spatial distribution characteristics of Cu, Zn, Ni and Cr contents were basically the same, which were similar to the distribution of basic volcanic rocks in the study area. The evaluation results of heavy metal geo-accumulation index showed that the concentration of Cd in the soil was the highest, and the soil was greatly affected by Cd, followed by Cr, and other heavy metals were less affected. The potential ecological risk levels of soil heavy metal pollution were mainly mild and moderate risk levels, while As, Pb, Cr and Zn were slight ecological risks, and the potential ecological harm was small. The above points of Cd, Hg and Ni intensity ecological risk accounted for 52.6%, 15.8% and 5.3% respectively. The potential ecological risk of soil heavy metals in the study area was mainly caused by Cd and Hg. Eight kinds of heavy metal elements were identified as three sources. Cu, Ni, Cr and Zn were mainly from natural sources, which were mainly affected by the high soil background value of basic volcanic parent rock, Pb, Cd, As and Hg were mainly from industrial sources and traffic sources. As was also affected by agricultural sources. The source of heavy metals in Haikou soil was relatively single. As a result, it is necessary to strengthen the pollution control of Cd, Cr and Hg in the soil, with the focus on the pollution control of Cd.