Marine dissolved organic matter (DOM) is one of Earth's largest long-term carbon reservoirs, critical to the global carbon cycle. A key breakthrough in understanding this pool is the identification of biorefractory carboxyl-rich alicyclic molecules (CRAM). Recent studies have challenged the biorecalcitrance of CRAM but lacked detailed molecular evidence. Using advanced online countergradient liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry to track microbial incubation, we revealed a wide spectrum of CRAM bioavailability regulated by molecular polarity. CRAM with lower polarity were preferentially degraded, whereas microbial reworking led to production of higher-polarity CRAM, characterized by increased oxidation state, nitrogen content, and aromaticity. Some microbially transformed CRAM were frequently detected in a global DOM dataset of 1485 seawater samples, suggesting their potential persistence in marine environments. This study provides molecular insights into the biorecalcitrance and transformation pathway of CRAM, underscoring the complexity and dynamic nature of marine organic carbon cycling.