Decreased bone mineral density (BMD) is common in patients with schizophrenia; however, the pathogenesis is unclear. Different classes of antipsychotic agents may affect BMD. This study systemically examined the effects of clozapine vs. other antipsychotics, and several hormonal and metabolic factors that may contribute to BMD in female patients with schizophrenia, who are more vulnerable than males. Forty-eight women with schizophrenia, treated with long-term antipsychotics of the prototype prolactin-sparing (PS) antipsychotic agent clozapine vs. prolactin-raising (PR) antipsychotics were enrolled. They were matched for demographic and clinical characteristics. Various factors, including blood levels of prolactin and sex hormones, psychopathological symptoms, global assessment of functioning, physical activity, and menopausal status, were determined to explore their contribution to low BMD (LBMD), defined as a dual-energy X-ray absorptiometer (DEXA) T score <−1. Overall, women receiving clozapine have better bone density than women receiving PR antipsychotics. Compared to PR antipsychotics, PS clozapine therapy is a protective factor (odds ratio 28.2, 95% confidence interval 2.37–336.10, p=0.008) for LBMD. Predictors for higher bone density in the clozapine group included higher clozapine dose (p<0.001), younger age (p<0.001), and higher thyroid-stimulating hormone level (p<0.001); in the PR group, higher body mass index (p=0.003) and lower alkaline phosphatase level (p=0.007) were associated with LBMD. This study suggests that clozapine treatment is beneficial for BMD compared to PR antipsychotic treatment in women with chronic schizophrenia, and clozapine's bone-density protecting effect is dose-related.