Photon-counting analysis plays a key role in many areas, such as biology, chemistry, and medicine. In this paper, we present an integrated time-correlated single photon counting (TCSPC) lifetime analytical system with a complete signal path-from fluorophore excitation, emission detection, to lifetime extraction. The time-to-digital module of the proposed TCSPC system achieves a root-mean-square differential non-linearity of 4% of the least significant bit and a full width at half maximum temporal resolution from 121 to 145 ps within the 500-ns full-scale range. To evaluate the lifetime extraction and detection limit of the proposed TCSPC system, a wide variety of samples, such as fluorescein in water, coumarin 6 in dimethyl sulfoxide, and rhodamine 6G in water, each prepared in 14 concentrations from 0.5 nM (nanomolar, 10 −9 mol/L) to 25 µM (micromolar, 10 −6 mol/L), are tested. With the optimized hardware and firmware design, the proposed TCSPC system can accurately extract the fluorescence lifetime of fluorescein, coumarin 6, and rhodamine 6G down to the concentration of 1, 1, and 2.5 nM, respectively, significantly outperforming similar fluorescence lifetime analysis systems. INDEX TERMS Non-invasive optical analysis, time-correlated single photon counting, low detection limit, fluorescence lifetime extraction.