Substitution of a single atom in a photoactive system is capable of vastly altering its optoelectronic properties leading to the generation of an efficient photocatalyst. In this study, we explore the impact of two-fold single-atom substitutions on the optoelectronic properties and photocatalytic performance of donor-acceptor type conjugated microporous polymers (D-A CMPs). For this, three isostructural triphenylamine (TPA)-based D-A CMPs were synthesized namely PTPA-BT, PTPA-BS, and PTPA-PS containing 2,1,3-benzothiadiazole, 2,1,3-benzoselenadiazole and [1,2,5]selenadiazolo[3,4-c]pyridine as the acceptor moieties, respectively. Firstly, PTPA-BT and PTPA-BS were synthesized using the S to Se single-atom substitution strategy, followed by the synthesis of PTPA-PS employing a second C to N single-atom substitution. The effect of single-atom substitution demonstrated drastic changes in their band gap, conductivity, and charge carrier dynamics, which in turn impacted their photocatalytic activity, although the change in their porosity was not much pronounced. In terms of photocatalytic detoxification of sulfur mustards, the activities of D-A CMPs follow the trend: PTPA-BS > PTPA-PS > PTPA-BT. In comparison with PTPA-BT (containing C, S) and PTPA-PS (containing N, Se), PTPA-BS (containing C, Se) exhibits a higher photocatalytic activity towards the photooxidation of thioanisole with >99% conversion and ∼93% isolated yield under visible-light illumination, which is attributed to its lower interfacial charge transfer resistance, stronger photocurrent response, optimal band gap and higher activity to generate superoxide anion radicals. Therefore, the two-fold single-atom substitution strategy is crucial for optimizing D-A CMPs for the photocatalytic oxidation of aryl sulfides. This approach allows fine-tuning of the optoelectronic properties to enhance photocatalytic efficiency and performance.