Background. Endocrine disorders such as amenorrhea, lactation, and irregular menstruation caused by antipsychotics are common in female patients. How to reduce or eliminate these adverse reactions is a matter of concern. Objective. To evaluate the therapeutic effect of progesterone in combination with vitamin B6 in the treatment of antipsychotic-induced amenorrhea. Methods. In our hospital, from May 2019 to May 2021, 120 patients with amenorrhea caused by antipsychotics who underwent surgery were selected for this prospective study. The random residue grouping method divided them into a progesterone group (60 cases) and a vitamin B6 group (60 cases). Among them, the progesterone group was treated only with progesterone, while the vitamin B6 group was given progesterone in combination with vitamin B6. The differences in endocrine index, prolactin, uterine size, and endometrial thickness, effectiveness, and safety analysis of the progesterone and vitamin B6 groups of patients were observed and compared. Results. Before treatment, there was no change in the comparison of endocrine indexes between the progesterone and vitamin B6 groups (
P
>
0.05
). After 1 month of treatment, there were significant differences in estradiol, prolactin, and follicle-stimulating hormone between the progesterone and vitamin B6 groups of patients (
P
<
0.05
). After 1 month of treatment, there were significant differences in prolactin, uterine size, and endometrial thickness, and the vitamin B6 group was significantly lower than the progesterone group (
P
<
0.05
). The clinical efficiency of 95.00% in the vitamin B6 group was significantly higher than 83.33% in the progesterone group (
P
<
0.05
). There were no adverse reactions in the progesterone and vitamin B6 groups. Conclusion. The effectiveness of progesterone combined with vitamin B6 in treating amenorrhea caused by antipsychotics is significantly better than simple progesterone, which can effectively improve the endocrine condition of patients and provide a reference for the clinical treatment of amenorrhea caused by antipsychotics.