In the present study, we aimed to use metabolomics platforms to examine circadian-regulated neurotransmitters across a 24-h day and the effects of Uncaria administration on daily rhythmicity in order to establish a strategy for evaluating the spatiotemporal efficacy evaluation strategy of Uncaria. By using targeted ultrahigh performance liquid chromatography-mass spectrometry metabolomics, we quantified 32 neurotransmitter metabolites every 4 h over 24 h. To assess 24-h metabolite rhythmicity, we performed cosinor analysis. The expression of hypothalamic rhythm genes was detected by reverse transcription polymerase chain reaction (RT-PCR). Data revealed circadian loss of many neurotransmitters during the entire circadian cycle in the serum of group M, indicating that hypertension causes circadian rhythm disorders. Cosinor analysis of the rhythmic oscillations of the levels of 32 neurotransmitters in the three groups showed that the metabolite rhythms peaked at approximately the same time of day (ZT4 and ZT16). Moreover, the amplitudes of the metabolite rhythms were altered. After treatment with Uncaria, the amplitudes of 13 neurotransmitters reverted to normal. The change trends in the hypothalamic rhythm genes confirmed the rhythm changes in neurotransmitters. Collectively, a novel pharmacodynamic evaluation strategy was established to dynamically observe the holistic effects of Uncaria on 32 circulating neurotransmitters within 24 h from the perspective of time dimension.