Centropages tenuiremis is a species with a wide distribution range in disturbed coastal waters. However, due to a lack of dietary information, it remains unclear as to how they maintain such dominance in fluctuating conditions. In this study, C. tenuiremis was collected from the Daya Bay Nuclear Power Plant both in inlet and outfall regions at 06:00, 12:00 and 18:00 on April 27, 2011 and their in situ diet was analyzed using a PCR protocol targeting 18S ribosomal genes. Thirty-four species of prey organisms were identified totally, including Dinophyta, Baciliariophyta, Viridiplantae, Rhizaria, Apicomplexa, Chordata, Mollusca, Arthropoda and Fungi, indicating an obvious omnivorous feeding habit of C. tenuiremis. Centropages tenuiremis obviously exhibited spatial and temporal variations in diet composition. More plant prey (land plants and phytoplankton) were consumed in the morning (~50%), while more animal prey (metazoans and protozoans) were ingested at midday and night (60%–70%). Furthermore, a more diverse diet was detected in the outfall region (10–11 taxa), where the temperatures were relatively higher and more fluctuating, than in the control region (5–10 taxa). This finding indicated that C. tenuiremis could potentially expand its food spectrum under stressful condition. Specifically, C. tenuiremis exhibited phytoplankton preference (58.62%–67.64%) in the outfall region with a lower omnivory index (0.27–0.35) than in the control region (0.51–0.95). However, phytoplankton density was lower than that in the control region, suggesting a possible herbivorous tendency of C. tenuiremis under elevated temperatures to balance the energy acquirement and feeding effort. The flexible food choices of C. tenuiremis observed here could effectively buffer environmental fluctuations and might be an important survival strategy in coastal ecosystems.