The Pearl River Delta Economic Zone (PRDEZ) is one of the most developed areas economically and socially in China, and its ecogeochemical environment is heavily affected by human activities. In this paper, net flux of soil heavy metals is estimated on regional inputoutput flux model, and then prediction and earlywarning forecast on geochemical accumulation of soil heavy metals is carried out. Early warning forecast is conducted by the factor pollution index obtained from the Probability Kriging model which integrates the space distribution and probability distribution of soil heavy metals. The concentration threshold for warning factor is taken from the China National Environmental Quality Standards for the levelII soil. It is shown that Cd, Hg, Ni and Cr are the main ecogeochemical warning factors for the paddy land soil, Cd, Hg and Ni factors for the dry land, and As, Cr and Ni for the garden land. With the present development model going until the year of 2025, the heavily warning regions of paddy land soil will extend to the Pengjiang District, Jianghai District and Xinhui District in Jiangmen City, Kaiping, Heshang, Zhongshan, Nansha Districts, Panyu District in Guangzhou City, Dinghu District, Duanzhou District and Gaoyao District in Zhaoqing City, and Doumen District in Zhuhai City. The heavily warning regions of dry land soil will extend to Panyu District, Nansha District, Baiyun District, Huangpu District, Luogang District and Huadu District in Gangzhou City, Gaoming District, Nanhai District, Shunde District and Shancheng District in Foshan City, Sihui District in Zhaoqing City, Xiaolan District, Guzhen District, Sanjiao District and Dongshen District in Zhongshan City, Doumen District and Jinwandeng District in Zhuhai City, and Xinhui, Kaiping and Taishan in Jiangmen City. The heavily warning regions of garden land soil will extend to Nansha District, Panyu District and Huadu District in Guangzhou City, the northern Huidong County in Huizhou City, Doumen District, Jinwan District and Tanzhou District in Zhuhai City, and Shunde District, Nanhai District, Shancheng District and Sanshui District in Foshan City.