(1) Background: Primary health care institutions (PHCI) play an important role in reducing health inequities and achieving universal health coverage. However, despite the increasing inputs of healthcare resources in China, the proportion of patient visits in PHCI keeps declining. In 2020, the advent of the COVID-19 pandemic further exerted a severe stress on the operation of PHCI due to administrative orders. This study aims to evaluate the efficiency change in PHCI and provide policy recommendations for the transformation of PHCI in the post-pandemic era. (2) Methods: Data envelope analysis (DEA) and the Malmquist index model were applied to estimate the technical efficiency of PHCI in Shenzhen, China, from 2016 to 2020. The Tobit regression model was then used to analyze the influencing factors of efficiency of PHCI. (3) Results: The results of our analysis reflect considerable low levels of technical efficiency, pure technical efficiency, and scale efficiency of PHCI in Shenzhen, China, in 2017 and 2020. Compared to years before the epidemic, the productivity of PHCI decreased by 24.6% in 2020, which reached the nadir, during the COVID-19 pandemic along with the considerable reduction of technological efficiency, despite the significant inputs of health personnel and volume of health services. The growth of technical efficiency of PHCI is significantly affected by the revenue from operation, percentage of doctors and nurses in health technicians, ratio of doctors and nurses, service population, proportion of children in the service population, and numbers of PHCI within one kilometer. (4) Conclusion: The technical efficiency significantly declines along with the COVID-19 outbreak in Shenzhen, China, with the deterioration of underlying technical efficiency change and technological efficiency change, regardless of the immense inputs of health resources. Transformation of PHCI such as adopting tele-health technologies to maximize primary care delivery is needed to optimize utilization of health resource inputs. This study brings insights to improve the performances of PHCI in China in response to the current epidemiologic transition and future epidemic outbreaks more effectively, and to promote the national strategy of Healthy China 2030.