Identification of cell SOC (state-of-charge) inconsistency for LiFePO4 battery packs is challenging due to the demanding conditions in hybrid electric vehicles (HEVs) and the relatively flat SOC–OCV (open circuit voltage) curve of LiFePO4 cells compared to others. We experimentally investigate cell voltages in a small battery pack and propose a Mean-plus-Difference Model (M+D Model). The M+D Model uses a cell mean model (CMM) representing the overall performance of the pack in high frequency. Meanwhile cell voltage differences (CVDs) between cells and the “mean cell” are studied by a cell difference model (CDM) in low frequency. A CDM considering SOC and internal resistance differences is subsequently presented and OCV differences are estimated. We further propose an SOC strategy to accurately identify cell SOC inconsistency by intermittently lowering pack SOC to 30% during HEV operation. Finally we discover that SOC differences can be determined with estimated OCV differences using SOC-difference/OCV-difference curve. The proposed method is verified by simulation and experiment. With the proposed method, LiFePO4 cell SOC inconsistency can be precisely estimated with existing measuring technology during HEV operating and cell equalization can be ultimately implemented.