In this study, a polluted farmland in eastern Zhejiang province was selected. Four treatments, including straw returning, straw non-returned, straw returning+lime, and straw non-returned+lime were set up. The dynamic monitoring of heavy metals in soil, straw, cereals, and vegetables was carried out for nine years. The results showed that the accumulation of heavy metals in rice straw, grain, and vegetable was significantly reduced by applying lime in polluted farmland, but the effect of applying lime on the content of total heavy metals in soil was not obvious. The effect of applying lime on the reduction of heavy metals in rice straw, grain, and vegetable was gradually weakened with the experimental time. Compared with straw non-returned, straw returning had less effect on the accumulation of heavy metals in soil, rice straw, and vegetable in a short time. However, the accumulation of cadmium and mercury in soil and the accumulation of cadmium, lead, and mercury in rice straw and vegetable after 4~5 years were significantly lower in straw non-returned farmland than that in straw returning farmland, and the effect on the accumulation of lead in soil was less. With the increase of test time, the difference of heavy metal accumulation in soil, rice grain, and vegetable between straw returning farmland and straw non-returned farmland gradually increased. The content of soil organic matter and available potassium in straw returning farmland was higher than that in straw non-returned farmland. It was concluded that long-term application of straw returning in cadmium and mercury polluted farmland was not conducive to the improvement of agricultural product quality, and the heavy-polluted rice straw returning should be controlled.