This study proposed label-free fluorescence lifetime imaging and phasor analysis methods to discriminate different grades of cervical intraepithelial neoplasia (CIN). The human cervical tissue lesions associated with cellular metabolic abnormalities were detected by the status changes of important coenzymes in cells and tissues, reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD). Fluorescence lifetime imaging microscopy (FLIM) was used to study human cervical tissues, human cervical epithelial cells, and standard samples. Phasor analysis was applied to reveal the interrelation between the metabolic changes and cancer development, which can distinguish among different stages of cervical lesions from low risk to high risk. This approach also possessed high sensitivity, especially for healthy sites of CIN3 tissues, and indicated the dominance of the glycolytic pathway over oxidative phosphorylation in high-grade cervical lesions. This highly adaptive, sensitive, and rapid diagnostic tool exhibits a great potential for cervical precancer diagnosis.