Birth defects are an important factor for the quality of newborn population. With the development of molecular genetic technology, an increasing number of genetic disorders leading to birth defects can now be detected. The lack of the knowledge for the basics and clinical applications of molecular genetic techniques have emerged as a shortcoming for primary care physicians who have formed the first tier prevention for birth defects. Currently, government has paid more attention to the above problems and formulated more training programs for primary obstetricians and gynecologists, e.g., "Prenatal Screening and Prenatal Diagnosis Post Training Program", "National Birth Defects Training Program", "National Primary Obstetrician Training Program". To some extent, such programs have met the urgent need for birth defect prevention in primary hospitals. But at the same time, some problems have also emerged. For instance, the knowledge for birth defects among primary obstetricians and gynecologists is poor, and there is lack of young personnel. This article has aimed to discuss the strategies to systematically improve the ability for preventing birth defects among primary care physicians by analyzing the obstacles and challenges for primary obstetricians and gynecologists in the era of molecular genetic testing.