Anthocyanins in plants play an important role in modulating human health. The cultivation of rice varieties rich in anthocyanins is inevitable to fulfil the demand for developing green and healthy agricultural practices in the future. However, the current genetic resources related to anthocyanin content in rice pericarp are still limited. This is not conducive to germplasm innovation and genetic improvement of colored rice varieties. To comprehensively explore the genetic resources regulating anthocyanin content in rice pericarp, noninvasive detection of anthocyanin was combined with genome-wide association analysis. Using this approach, 13 QTLs associated with anthocyanin content in the pericarp were detected in 533 rice germplasms. These QTLs included 17 candidate genes in addition to Rc, Rd, Rb, and OsMYB3. Through the analysis of homology and expression patterns of these candidate genes, eight MYB and one bHLH gene were preliminarily identified as novel candidate genes associated with anthocyanin content in rice pericarp. This study comprehensively analyzed the genetic basis of anthocyanins in rice pericarp for the first time, providing a theoretical basis and identifying novel genetic resources for the breeding of healthy functional rice varieties.