Background: To enhance the efficacy of maternal serum screening (MSS), we conducted an analysis to examine the correlation between certain factors identified during second-trimester screening (STS) and fetal chromosomal abnormalities, excluding the common trisomies (trisomies 13, 18, and 21). Additionally, specific risk factor ranges were established for each category. Methods: A retrospective 1:3 matched case-control study was conducted. Case data were obtained from 311 STS samples of fetal chromosomal abnormalities other than common trisomies, with testing performed in the Prenatal Diagnosis Center of the Maternal and Child Health Care Hospital of Sichuan Province in China between 6 January 2013 and 12 April 2023. A total of 933 controls were matched accordingly. Univariate and multivariable conditional logistic regression analyses were implemented and sensitivity analysis was performed. Results: Multivariable logistic analyses revealed that the independent risk factors for fetal chromosomal abnormalities other than common trisomies were ultrasonographic structural abnormalities (odds ratio (OR) = 3.038; 95% confidence interval (CI), 1.774–5.202; p < 0.001); free β-human chorionic gonadotropin (free β-hCG) as multiples of the median (MoMs) of ≤0.34 (OR = 3.006; 95% CI, 1.803–5.013; p < 0.001), 2.82–3.53 (OR = 1.884; 95% CI, 1.321–2.688; p < 0.001), 3.54–4.67 (OR = 1.949; 95% CI, 1.300–2.923, p = 0.001), and ≥4.68 (OR = 1.730; 95% CI, 1.045–2.866; p = 0.033); and a trisomy 21 (T21) risk of 1/271–1/1000 (OR = 2.434; 95% CI, 1.706–3.472; p < 0.001), 1/101–1/270 (OR = 3.330; 95% CI, 2.300–4.821; p < 0.001), and ≥1/100 (OR = 3.441; 95% CI, 2.178–5.438; p < 0.001). Conclusions: Ultrasonographic structural abnormalities, free β-hCG MoMs, and T21 risk were identified as independent risk factors for fetal chromosomal abnormalities (with the exception of common trisomies) in STS. Our findings thus provide data to support clinical decision-making.