Currently, safety issue on Li-ion battery caused by thermal stability is one of the main factors that restricts its developmental application. In this paper, from a perspective of heat generation, we present a method to estimate remaining capacity of single Li-ion battery. Sample entropy (SampEn) is employed for the calculation of surface temperature in charging process and the relationship between SampEn and capacity fading in aging process is built. Considering various factors of capacity attenuation, an intelligent estimation approach is proposed by the combination of SampEn and particle filter (PF).