Photocatalytic degradation of antibiotics from wastewater by polymeric photocatalysts is a powerful strategy to alleviate ecological damage and environmental pollution. Conjugated microporous polymers (CMPs) are promising in photocatalysis due to their tunable electronic structure and excellent light absorption. Nonetheless, CMPs still suffer from low exciton separation efficiency. Here, we propose a molecular isomerism strategy to promote exciton dissociation in CMPs by modulating the position of the carbonyl moiety. As a result, the introduction of carbonyl moiety with different substitution positions into the backbone of CMPs could minimize the exciton binding energy (E_b) and thus promote charge separation. PyCMPs-3 with phenanthrenequinone moiety as the acceptor featured a lower E_b of 37.19 meV, which are much smaller than that of carbonyl-free PyCMPs-1 (80.49 meV) and PyCMPs-2 (59.21 meV) with anthraquinone as the acceptor. Among them, PyCMPs-3 performed the best in photocatalytic degradation of ofloxacin (99 %) at a concentration of 144 ppm, which was significantly higher than that of its analogues PyCMPs-1 (26 %) and PyCMPs-2 (57 %) within 100 min under visible light exposure. In short, this work delivered a novel molecular isomerism strategy to minimize E_b by regulating the position of the carbonyl moiety for enhancing the photocatalytic degradation efficiency, promoting the development of CMPs for practical environmental remediation applications.