Objective To compare the advantages and disadvantages between high performance liquid chromatography (HPLC)-ultraviolet (UV, HPLC-UV), HPLC-fluorescence detector (FLD, HPLC-FLD) and HPLC-mass spectrometry (MS, HPLC-MS) for determination of the monoamine neurotransmitters (MNs) in brain tissues of mice, and to determine the content of MNs in brain tissues of vascular depression mice using the optimal method. Methods We used the UV, FLD and MS detectors to establish different methods for determination of dopamine (DA), norepinephrine (NE) and 5-hydroxytryptamine (5-HT) in brain tissues. Then the methods was verified with methodology. The HPLC-FLD was applied for the content determination of DA, NE and 5-HT in different brain tissues of vascular depression mice. Results It was observed that the limits of quantification for HPLC-UV, HPLC-FLD and HPLC-MS were DA 103.5 ng/mL, NE 107.5 ng/mL and 5-HT 93.6 ng/mL; 10.35 ng/mL, 10.75 ng/mL and 9.36 ng/mL; and 10.35 ng/mL, 32.25 ng/mL and 9.36 ng/mL, respectively. Both HPLC-FLD and HPLC-MS for DA and 5-HT were superior to HPLC-UV. HPLC-FLD for NE was superior to HPLC-MS. Compared with HPLC-UV and HPLC-FLD, HPLC-MS showed remarkable matrix effects. HPLC-FLD determination results showed that content of DA was the lowest in hippocampus, 5-HT was the lowest in cerebral cortex, and NE did not differ in different brain tissues of vascular depression mice. Conclusion Compared with HPLC-UV and HPLC-MS, HPLC-FLD can more effectively determine the contents of MNs (DA, NE and 5-HT). DA and 5-HT can be used as the diagnostic markers of the vascular depression diseases.