The 5-Hydroxytryptamine (5-HT) level determination is crucial for predicting, pathogenesis, diagnosis, and pharmacological treatment of schizophrenia. To realize the extraction of trace 5-HT in complex matrix samples, a magnetic molecularly imprinted solid-phase extraction (MMISPE) pretreatment method was developed. In combination with UPLC-MS/MS, the method was possible to achieve the quantification of 1 ng/mL 5-HT in tissue samples. The type of adsorbent, magnetic surface molecularly imprinted polymers (MMIPs) adsorbent dosage, adsorption temperature, and adsorption method were screened to obtain the better extraction of 5-HT. After optimizing the extraction and separation method, we applied the MMISPE method to the detection of 5-HT in peripheral blood of clinical schizophrenia patients. The results showed that the average concentration of 5-HT in the peripheral blood of healthy controls was 74.30 ng/mL, whereas the 5-HT content in the samples from schizophrenic patients was 1.17 ng/mL.