Cadmium (Cd), a non-essential and toxic heavy metal element, is extremely harmful for rice growth, food safety and even public health. In this paper, two rice varieties, Shanyou 63 (Tolerant to Cd stress) and Nipponbare (Susceptible to Cd stress), were employed as materials to investigate the protein expression and protein-protein interaction in rice in response to different stages of Cd stress. The result showed that Cd accumulated in the root of both rice cultivars, but the Cd content in the root of Shanyou 63 was significantly lower than that in Nipponbare. Eight proteins were up-regulated in the two rice cultivars, but the expressing abundance of these eight proteins in Shanyou 63 was statistically higher than that in Nipponbare, indicating that the relative abundance of these eight proteins was positively related to the ability of rice cultivars to avoid Cd stress. According to Gene Ontology annotation, four of these eight proteins were involved in energy metabolism, while four participated in stress tolerance. Native-PAGE and LC-MS/MS methods revealed that four GSTs, one cysteine synthase and one protein disulfide isomerase formed a stable protein complex in Shanyou 63 root in response to 3-, 5-and 7-day Cd stresses, but this protein complex did not appear in Nipponbare root under Cd stress. Owing to the same domain, the four glutathione S-transferases (GSTs) and cysteine synthase had the potential to interact and compose a protein complex to detoxify Cd in Shanyou 63 rice plants. Our results provide new insight into the detoxification mechanism of rice plant in response to Cd stress and may prove to be useful for the future research.