Lateral roots (LRs) are the main organ for tea plant to absorb soil moisture and nutrients. Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. LRs formation and development are limited by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in LRs of tea plant treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of genes expression; thus, regulated lateral roots formation. Furthermore, metabolisms of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant LRs formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. This study provides new insights into the mechanisms associated with nitrogen-auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level