Carbon nanodots (C-dots) are emerging as a new type of promising agent in anticancer, imaging, and new energy. Reports as well as the previous research indicate that certain C-dots can enhance targeted cancer therapy. However, in-depth mechanisms for such anticancer effect remain unclear. In this work, treatment provided by the date pit-derived C-dots, exhibits significant DNA damage; Annexin V/7-AAD-mediated apoptosis, and G2/M cell cycle arrest in prostate cancer cells. The application of C-dots to the cell generally leads to acidulation of the cell medium, cooperated with membrane compact. The date pit-derived C-dots are observed inhibiting the horseradish peroxidase. Moreover, the C-dots disrupt likely through nucleotide excision DNA repair at low dose during DNA ligation step suggesting the antimicrobial effect and targeting Pim-1, EGFR, mTOR, and DNA damage pathways in cancer cells. For the first time the detailed and novel mechanisms underlying the C-dots, derived from the date-pit, as an efficient, low-cost, and green nanomaterial are reveled for cancer therapy and anti-infection.