Photochemical active species generated from photosensitizers, e.g., dissolved organic matter (DOM), play vital roles in the transformation of micropollutants in water. Here, butanedione (BD), a redox-active moiety in DOM and widely found in nature, was employed to photo-transform naproxen (NPX) with peracetic acid (PAA) and H2O2 as contrasts. The results obtained showed that the BD exhibited more applicable on NPX degradation. It works in the lake or river water under UV and solar irradiation, and its NPX degradation efficiency was 10–30 times faster than that of PAA and H2O2. The reason for the efficient transformation of pollutants is that the BD system was proved to be a non-free radical dominated mechanism. The quantum yield of BD (Ф254 nm) was calculated to be 0.064, which indicates that photophysical process is the dominant mode of BD conversion. By adding trapping agents, direct energy transfer from 3BD* to NPX (in anoxic environment) or dissolved oxygen (in aerobic environment) was proved to play a major role (> 91 %). Additionally, the BD process reduces the toxicity of NPX and promotes microbial growth after irradiation. Overall, this study significantly deepened the understanding of the transformation between BD and micropollutants, and provided a potential BD-based process for micropollutants removal under solar irradiation.