This study investigated the contents and speciation of the heavy metals As, Cd, Hg, Cr, Pb, Cu, and Zn in a chicken manure-compost-soil-apple system. As, Cd, and Hg concentrations in chicken manure samples exceeded the National Agricultural Standard for Organic Fertilizers of China. Moreover, the composting process further increased heavy metal concentrations in the chicken manure. However, the composting process also changed the speciation of the heavy metals. In orchard soils that used chicken fertilizer compost for long periods, Cd and Hg concentrations exceeded the required limits for orchards stipulated by the Environmental Quality Standard for Soils of China. As, Cd, and Hg heavy metal concentrations in the apple fruit also exceeded food pollutant limits specified by the National Food Safety Standard, especially for Hg, which was 25 times above the allowable limit. As, Cd, and Hg concentrations in chicken manure, compost, soil, and apple fruit all exceeded standard levels (except for As in soil), while the remaining heavy metals (Cr, Pb, Cu, and Zn) were below the standard. This implies a correlation between the migration and accumulation of heavy metals in the chicken manure-compost-soil-apple system.