The endogenous fluorophores such as reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and flavin adenine dinucleotide (FAD) in cells and tissues can be imaged by fluorescence lifetime imaging microscopy (FLIM) to show the tissue morphology features, as well as the biomolecular changes in microenvironment. The two important coenzymes in cellular metabolism, NAD(P)H and FAD, can be used to monitor the cellular metabolic status. This work proposed a novel method to study the uterine metabolism at the adjacent site of healthy cervix. It was found that the benign uterine tumors such as leiomyomas and adenomyosis with abnormal cell growth can be detected by measuring the fluorescence lifetime of NAD(P)H and FAD in adjacent healthy cervical tissues. This method opened a novel strategy for afflicted women to undergo the cervical biopsies instead of hysterectomies for detecting tumors, which can preserve the fertility of patients. The FLIM studying on NAD(P)H and FAD indicated the correlation between metabolism and some diseases, including diabetes, hyperthyroidism and obesity. It was also suggested that the metabolic level might be quite different for a patient with a malignant tumor history.