In high-latitude areas, lithium-ion batteries for electric vehicles frequently operate under low-temperature conditions. However, lithium-ion battery suffers from complex energy loss and performance degradation under low temperature. In order to quantify the degradation mode of the battery, this paper proposes a framework with electrochemical theory and electrode 3-D morphology. The proposed framework mainly includes two parts: Firstly, the degradation modes (DMs) of the battery are extracted from incremental capacity (IC), differential voltage (DV) techniques and electrochemical impedance spectroscopy (EIS). Secondly, the 3-dimension (3-D) morphological calculation method is proposed to analyze the degradation situation of the battery electrodes. Then, the battery aging and performance testing system under low temperature is established to verify the effectiveness of the proposed framework from the perspective of surface morphology. In order to validate the effectiveness of the proposed framework, an experimental bench for battery low-temperature aging and performance testing is constructed. The experimental results demonstrate that: (1) Battery capacity is greatly reduced at low temperatures, and loss of lithium inventory (LLI) is greater at low temperatures (−5 °C and −10 °C) than at 25 °C under the same state of health (SOH). (2) By analyzing 3-D morphology, the low temperature can lead to a significant change in the surface roughness parameters of the anode electrode. The low temperature aggravates the reduction of anode gap area. It is found that the microscopic mesomorphic changes are closely related to the aging of the battery. (3) The anode graphite (002) peak position is shifted to a low angle of 2.2° under low temperature. Scanning electron microscope (SEM) images shows the graphite anode is covered by a lithium-rich SEI at low temperature. (4) Post-test calculations of the consistency of the relevant covariates revealed that the electrochemical and morphological covariates are highly linearly correlated, respectively. Hence, the effectiveness of the proposed framework is verified and a novel perspective is provided to reveal the battery performance degradation under low temperatures, which can help guarantee safe operation through battery management system.