Phenolics are key components for plant survival and have important medicinal uses for human beings. Nevertheless, the approach for identifying all four types of phenolics is still in need by now. In this study, we developed an approach to elucidate all these phenolics, including anthocyanins, flavanols, chlorogenic acid-related compounds and hydroxycinnamate derivatives in plants, taking purple tomato as material. We identified 58 phenolics and addressed their structures. Among them, there were 15 anthocyanins, 30 flavanols, 8 chlorogenic acid-related compounds and 5 hydroxycinnamate derivatives. In tomato, 29 out of 58 phenolics were not reported previously. By quantification, it was found that the total phenolics were more concentrated in the fruit peel, compared to plant leaves and the fruit flesh. Based on these phenolics, we proposed five possible pathways in flavonols, anthocyanins and hydroxycinnamate derivatives. These findings provide new insight into identification and metabolic variation of phenolics in plants.