5-Methylcytosine (5mC) is the predominant epigenetic modification of DNA. 5mC and its sequential oxidation product, 5-hydroxymethylcytosine (5hmC), are crucial epigenetic markers which have a profound impact on gene stability, expression, and regulation. In the present work, ab initio electronic structure computations were performed to investigate the excited-state decay pathways for 5mC and 5hmC in both the neutral and protonated forms. Based on the theoretical quantities, four nonradiative decay pathways via conical intersections (CIs) were identified: ring distortion, ring opening, N-H dissociation, and intersystem crossing (ISC) pathways. Additional calculated potential energy surfaces revealed that ring distortion and ISC pathways were the most effective routes for 5mC and ShmC, respectively. The influence of environmental factors, such as the solution and an acidic environment, was also explored in this study. Our study demonstrated that excited-state decay pathways via CIs are indispensable for the photostability of DNA epigenetic modifications and may be involved in ingenome stability and mammalian development.