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Light is the key factor affecting the synthesis of anthocyanins in pepper. In this study, pepper fruit under different light days was used as experimental material to explore the synthesis of anthocyanins in purple pepper. A total of 38 flavonoid metabolites were identified in the purple pepper germplasm HNUCA21 by liquid chromatography–tandem mass spectrometry (LC-MS/MS), of which 30 belong to anthocyanins. The detected anthocyanin with the highest content was Delphinidin-3-O-glucoside (17.13 µg/g), which reached the maximum after 168 h of light treatment. Through weighted gene co-expression network analysis (WGCNA), the brown module was identified to be related to the early synthesis of anthocyanins. This module contains many structural genes related to flavonoid synthesis, including <i>chalcone synthase</i> (<i>CHS</i> 107871256, 107864266), <i>chalcone isomerase</i> (<i>CHI</i> 107871144, 107852750), <i>dihydroflavonol 4-reductase</i> (<i>DFR</i> 107860031), <i>flavonoid 3′ 5′-hydroxylase</i> (<i>F3’5’H</i> 107848667), <i>flavonoid 3′-monooxygenase</i> (<i>F3M</i> 107862334), <i>leucoanthocyanidin dioxygenase</i> (<i>LDOX</i> 107866341), and <i>trans-cinnamate 4-monooxygenase</i> (<i>TCM</i> 107875406, 107875407). The module also contained some genes related to anthocyanin transport function, such as <i>glutathione S-transferase</i> (<i>GST</i> 107861273), <i>anthocyanidin 3-O-glucosyltransferase</i> (<i>UDPGT</i> 107861697, 107843659), and <i>MATE</i> (107863234, 107844661), as well as some transcription factors, such as <i>EGL1</i> (107865400), <i>basic helix-loop-helix 104</i> (<i>bHLH104</i> 107864591), and <i>WRKY44</i> (107843538, 107843524). The co-expression regulatory network indicated the involvement of <i>CHS</i>, <i>DFR</i>, <i>CHI</i>, and <i>EGL1</i>, as well as two <i>MATE</i> and two <i>WRKY</i><i>44</i> genes in anthocyanin synthesis. The identified genes involved in early, middle, and late light response provided a reference for the further analysis of the regulatory mechanism of anthocyanin biosynthesis in pepper.