Abstract: Neurological diseases, cardiovascular diseases, and pulmonary diseases have always been major threats to human health. How to intuitively, efficiently, and rapidly screen out drugs with therapeutic effects is a key scientific issue in the field of biomedicine that urgently needs to be addressed. In this study, aiming at the pathological characteristics of these three types of diseases, key gene promoters such as those of nerve growth factor, vascular regeneration and repair factors and pneumonia factors were cloned and linked to reporter genes for quantification. Finally, a molecularly targeted drug screening model based on the stem cell differentiation system was constructed, and its function was verified by applying known pathway activators. This model not only has the universal characteristic of predicting the efficacy of compounds, but also can achieve dynamic analysis of the relationship between time and efficacy as well as the relationship between dosage and efficacy in view of the complex characteristics of traditional Chinese medicines and their compound ingredients, effectively revealing the material basis of their efficacy and providing important technical support for the quality control of subsequent clinical medications. While maintaining the advantages of traditional screening methods, this model breaks through the limitations of existing technologies. Finally, we discuss the technical characteristics of existing drug screening models and conduct a prospective discussion on the application prospects of this model in the field of drug research and development. The animal welfare and experimental procedures of the work were approved by the Medical Ethics Committee of Southwest Jiaotong University approval No. SWJTU-2403-NSFC(026).