Rice can accumulate more organic and inorganic arsenic (iAs) than other crop plants. In this study, the localization of As in rice grains was investigated using High Performance Liquid Chromatography-Inductively Coupled Plasma Mass Spectrometry (HPLC-ICP-MS) based on 26 rice varieties collected from two provinces. In all the samples, the total As contents in polished rice were 0.03–0.37 mg/kg, with average values of 0.28 and 0.21 mg/kg for two sample sets. The results of the determination of arsenic speciation in different components of rice grain showed that in the polished and brown rice the mean value of arsenite (As(III)) was nearly twice than that of arsenate (As(V)). The regional difference was observed in both total As contents and As speciation. The reason may be that As(III) is more mobile than As(V) in a dissociated form and because of soil properties, rice varieties, and the growing environment. The proportion of iAs and the total As in rice bran was higher than that in polished rice, and this is because As tends accumulate between the husk and the endosperm. In our study, selenium could alleviate the risk of arsenic toxicity at the primary stage of rice growth. Co-exposure to As and Se in germinated rice indicated that the reduction in As accumulation in polished rice reached 73.8%, 76.8%, and 78.3% for total As, As(III), and As(V) when compared with rice treated with As alone. The addition of Se (0.3 mg/kg) along with As significantly reduced the As amount in different parts of germinated rice. Our results indicated that Se biofortification could alleviate the As accumulation and toxicity in rice crops.