To address the intermittency problems of variable renewable energy (VRE) in low-carbon energy systems, flexibility has become increasingly important. Electrified transportation exhibits great potentialto provide essential flexibility. In this work, we analyzed and compared the flexibility values of battery electric vehicles (BEVs) and fuel cell electric vehicles (FCEVs) for planning and operating interdependent electricity and hydrogen supply infrastructures while considering battery degradation impacts and costs. A cross-scale framework involving both macro-level and micro-level models was proposed to compute the values of flexible EV charging. At the macro level, a sector-coupling planning model was adopted to estimate the system cost reduction from flexible EV charging incorporating battery degradation costs. Battery degradation cost computation for BEVs was based on micro-level simulations of battery degradation via a porous electrode theory-based model under various charging-time constraints and temperatures. The results show that the flexibility values of BEVs are significantly reduced by considering the battery degradation cost and becomes comparable to those of FCEVs. Fast charging and a low-temperature environment could reduce the flexibility values of BEVs due to increased degradation. Under theelectrolytic-hydrogen only pathway, with more stronglycoupled power and hydrogen supply chains, the flexibility values of BEVs are significantly reduced because of the substitution effect of the less expensive flexibility from hydrogen storage. Our findings imply that policies (e.g., the hydrogen pathway) and relevant management technologies (e.g., battery fast charging and thermal management) for BEV battery degradation mitigation are crucial to shaping the comparative flexibility advantage of the two transportation electrification pathways.