The state-of-charge (SOC) is a critical parameter of a Li-ion battery pack. Differences among in-pack cells are inevitable and can change the total capacity of a pack and the remaining available capacity. Because the traditional methods for the estimation of the SOC of a pack did not consider the difference among the cells and the impact of balance control, we developed a new method that accounts for these problems. To accurately estimate the pack SOC, we establish the relationship between the parameters of the pack and those of in-pack cells under different balance control strategies. This paper also studies the two different types of connections of a battery pack: in series and in parallel. Based on the model of the first over-charged cell and that of the first over-discharged cell, the estimation of the SOC of a battery pack is realized by the Unscented Particle Filter (UPF) algorithm. A simulation experiment verified the method for the estimation of the SOC for a battery pack based on actual data and proved that an accurate estimation value can be obtained by the method.