Background: Village doctors, as gatekeepers for the health of rural residents in China, are confronted with adversity in providing the basic public health services (BPHS), which has significantly impeded them from providing high quality BPHS. This study aimed to explore the obstacles and difficulties faced by village doctors in order to improve the quality and efficiency of BPHS provision and increase the health level of the population. Methods: In-depth interviews were employed to conduct this qualitative study. A total of 51 village doctors in four cities of Shandong Province were interviewed. The interviews were transcribed, anonymized, and imported into NVivo11.0 to facilitate management. Thematic framework analysis employing the constant comparison method was applied to the data analysis. Results: The main challenges faced by village doctors comprised the shortage, gender imbalance, and poor education of village doctors; older village doctors in some villages; low income; lack of social security; inappropriate performance assessment; inadequate professional BPHS training; heavy workload; and insufficient cooperation from rural residents, which have exacerbated the quality, efficiency, and accessibility of BPHS to some extent. Conclusions: Village doctors, as the important BPHS providers in rural Shandong, are facing a wide range of challenges. It is urgent for government officials and policy makers to consider these challenges and concentrate on improving the quality of BPHS provision by developing relevant and practical strategies.