Understanding the underlying catalytic mechanisms with nanometer resolution is of critical importance to the rational design of 1D heterogeneous catalysts. However, a fundamental investigation of photocatalytic activities and kinetics at their individual sites is still challenging. Herein, in situ single-molecule fluorescence microscopy is employed to study the site-specific catalytic activities and dynamics on 1D-1D heterostructure for the first time. For carbon nanotube (CNT)/CdS nanorod composites, it is found that the CdS end with heterojunction exhibits the highest catalytic conversion rate constant of resazurin photoreduction, which is 30%, 7%, and 19% higher than those of the middle segment and the bare end of CdS, and the CNT end with heterojunction, respectively. A similar trend of adsorption abilities is observed in these structures. Such phenomena can be attributed to the different content of defects in these structures. Regarding the dissociation behaviors, the dissociation rate constants of all structures exhibit an opposite trend to those of adsorption and conversion. The direct and indirect dissociation are found to be predominant on CdS and CNT, respectively. Such investigation provides a deep insight into the understanding of site-specific properties on 1D heterogeneous catalysts and helps construct the "structure-dynamics" correlations at the nanoscale.