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Anthocyanins are precious industrial raw materials. Purple corn is rich in anthocyanins, with large variation in their content between organs. It is imperative to find a rapid and non-destructive method to determine the anthocyanin content in purple corn. To this end, a field experiment with ten purple corn hybrids was conducted, collecting plant images using a digital camera and determining the anthocyanin content of different organ types. The average values of red (R), green (G) and blue (B) in the images were extracted. The color indices derived from RGB arithmetic operations were applied in establishing a model for estimation of the anthocyanin content. The results showed that the specific color index varied with the organ type in purple corn, i.e., AC_CR for the grains, BRT for the cobs, AC_CB for the husks, R for the stems, AC_CB for the sheaths and BRT for the laminae, respectively. Linear models of the relationship between the color indices and anthocyanin content for different organs were established with R² falling in the range of 0.64–0.94. The predictive accuracy of the linear models, assessed according to the NRMSE, was validated using a sample size of 2:1. The average NRMSE value was 11.68% in the grains, 13.66% in the cobs, 8.90% in the husks, 27.20% in the stems, 7.90% in the sheaths and 15.83% in the laminae, respectively, all less than 30%, indicating that the accuracy and stability of the model was trustworthy and reliable. In conclusion, this study provided a new method for rapid, non-destructive prediction of anthocyanin-rich organs in purple corn.