The present disclosure provides a method, portable device, and system for detecting physiological phenotype of crops, which determines a digital color chart according to the distance between a designated crop and the portable device and the present environmental brightness, and then determines that the appearance color of the designated crop belongs to which control color information of the selected digital color chart. It can avoid causing the error result because of the influence of the subjective determination and the environmental light. Therefore, the selected control color information may correspond to physiology information of the designated crop, to provide farmers with an understanding the present physiological phenotype of the designated crop.