Pig-biogas residue is widely used as organic fertilizer for rice (Oryza sativa L.) in China. To evaluate the risk of heavy metal contamination in paddy soil and rice grains caused by long-term pig-biogas residue fertilization, this study was conducted in paddy fields which had been fertilized continuously with pig-biogas residue for 8 years. We found that pig-biogas residues contained high concentrations of arsenic (As), cadmium (Cd), copper (Cu) and zinc (Zn). As a result, the concentrations of these four metals in paddy soils and rice grains sampled from biogas residue fertilized fields were significantly higher than those from control fields. In addition, in biogas residue fertilized fields, the concentrations of these four metals rapidly increased in the tillage layer compared with those in deep soil layers, and biological availability was significantly higher than in control fields. Moreover, we found that the accumulation of these four metals in paddy soils and rice grains increased in the second year compared with the first year. To reduce heavy metal accumulation in rice grains, we screened for rice genotype among 20 local rice genotypes. We found obvious genotypic differences in grains' accumulation of heavy metals, and identified some rice genotypes which had low accumulation of multiple heavy metals. These low-accumulating genotypes predicate the possibility to reduce heavy metal accumulation in rice grains grown in pig-biogas residue fertilized fields.