Abstract: In order to understand the transfer characteristics of heavy metals in farmland soil-crop system with low geochemical background, 30 paired rice grain and soil samples from 878 km² acid magmatic rock area outcropped in Qinbei district of Guangxi were collected. Specifically, the distribution of heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb and Zn) in the soils and rice grains, the fractionations and influencing factors on bioavailability of Cd and other metals in the soils were studied. The results showed that soil pH values in studied area ranged from 4.66 to 5.36, which was acidic. The concentrations of Cd, As, Cr and other heavy metals were all lower than or far below the risk screening values specified in Chinese soil environmental quality standard (GB15618-2018). In rice grains from the studied area, As, Cr, Hg and Pb did not exceed the standard; but for Cd an exceedance rate of 16.7% was observed. In soils, As and Pb mainly existed in the residual fraction, Hg mainly existed in the residual and strong organic binding fractions. Moreover, the bioconcentration factor (BCF) and bioavailability of Cd were the highest with 32% being the water soluble, ion exchangeable and carbonate binding fractions. The transfer of heavy metals from soil to rice grains is mainly related to soil pH value, Fe, Mn, and soil texture. Therefore, the ecological risk of heavy metals in farmland in acid magmatic rock area with low geochemical background is worthy of attention due to its acidic/strongly acidic soil with heavy metals being of low levels but high bioavailability.