Objective To investigate the status and training outcomes of trainees in birth defects prevention and control training programs, and to explore influencing factors. Methods A cross-sectional survey design was adopted. Trainees from birth defect prevention and control talent training programs across 13 prefecture-level cities in Jiangsu Province from 2022 to 2024 were selected as the study subjects. Information on basic demographics, self-evaluation (full score: 5), and training satisfaction was collected and analyzed for its correlation with the overall training assessment score (full score: 100). Data were processed using methods including one-way analysis of variance and Spearman′s test. Results A total of 378 trainees were included in this study. Among them, only 36 (9.5%) were aged ≤30 years; 201 trainees (53.2%) had ≤3 years of work experience related to birth defect prevention and control; 287 trainees (75.9%) held bachelor′s degrees and 88 (23.3%) held postgraduate degrees; 221 trainees (58.5%) were from tertiary hospitals. Trainees reported relatively high self-evaluations in five areas: policy and regulation knowledge, theoretical knowledge, practical skills, health education capabilities, and lifelong learning abilities [scores: (3.34 ± 0.85), (3.52 ± 0.78), (3.57 ± 0.73), (3.43 ± 0.72), (3.52 ± 0.69), respectively], while self-evaluation in scientific research and innovation capability was slightly lower [(2.64 ± 0.81)]. Trainees′ satisfaction scores regarding training curriculum design, teaching quality, and assessment methods were (4.49 ± 0.60), (4.57 ± 0.58), and (4.29 ± 0.65), respectively. The overall assessment score for trainees was (88.5 ± 7.9). No correlation was found between trainees′ professional title or years of related work experience and assessment scores (all P > 0.05). For trainees in prenatal screening and diagnosis, both educational level (ρ=0.262, P=0.009) and hospital level (ρ=0.325, P=0.001) showed positive correlations with assessment scores. Conclusions This training program has initially achieved broad coverage of trainees from diverse backgrounds and enhanced core competencies, with overall trainee satisfaction and assessment scores being favorable. However, scientific research and innovation capabilities among trainees remain insufficient, and while training outcomes overall show no direct association with trainees′ seniority, factors such as educational level still influence training effectiveness in certain specialties. Efforts should focus on strengthening the cultivation of scientific research and innovation capabilities, emphasizing professional differences, and further optimizing the training system to support the continuous improvement of birth defect prevention and control standards in our province.