Profiling of steroid hormones is incredibly valuable in clinical settings for diagnosing endocrine disorders. However, the presence of matrix effects and labor-intensive manual work in LC-MS/MS analysis has hindered its routine application. In the present study, a highly efficient and automated magnetic bead extraction method was developed to address matrix effects and quantitatively profile 15 steroid hormones in human serum. Octadecyl (C18) and N-vinylpyrrolidone divinylbenzene (HLB) modified magnetic beads were compared for enriching steroids from human serum. Following enrichment, the beads were separated using a magnetic field; the matrix was cleaned, and the steroid hormones were eluted from the beads for LC-MS/MS analysis. This entire process of enrichment, cleanup, and elution was conducted automatically, making it simple, fast, and cost-effective. The results indicated that steroid hormones could be selectively enriched from human serum in just 1 min using C18 magnetic beads. The absolute matrix effect, evaluated as the relative response between human serum matrix and methanol solution, ranged from 89.2% to 113.1% for low levels, from 82.3% to 112.0% for medium levels, and from 91.7% to 111.0% for high levels. The intrabatch coefficients of variation (CVs) and interbatch CVs were between 3.1% and 13.4% and between 3.0% and 13.7%, respectively. Recoveries were between 87.6% and 114.3% for low levels, 94.0% and 105.0% for medium levels, and 91.9% and 111.7% for high levels. The clinical application was demonstrated by profiling steroid hormones in 160 pregnant women at various gestational weeks. The results suggested that the automated magnetic bead extraction method for LC-MS/MS could effectively address matrix effects in profiling steroid hormones. To our knowledge, this is the first automated magnetic bead extraction method for LC-MS/MS profiling of steroid hormones in clinical practice.