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As different batteries exhibit their own advantages and disadvantages, a single-type battery system for a mobile embedded system (such as smartphones and tablet PC) cannot overcome the inherent limitations of its target battery. For example, although the lithium cobalt oxide (LCO) battery is the most popular battery for mobile embedded systems due to its high energy density, mobile embedded systems equipped with LCO batteries suffer from rapid capacity degradation. In this letter, we target heterogeneous batteries in a mobile embedded system and propose a method for minimizing the capacity degradation of the batteries. To this end, we first analyze factors that affect capacity degradation, and choose dominant factors that are controllable in a mobile embedded system. We then build a battery degradation model considering the factors, and finally develop a battery scheduling algorithm that minimizes capacity degradation using the degradation model. Our evaluation with real experiments and simulations demonstrates the effectiveness of the proposed algorithm in minimizing capacity degradation.