As a technical tool to guide the optimal allocation of healthcare resources, pharmacoeconomic evaluation has been gradually applied to national healthcare decisions, including the adjustment of the National Reimbursement Drug List in China. With the acceleration of drug market approval and access to insurance coverage, the demand for pharmacoeconomic evaluation in healthcare decision-making is also increasing. Designing a pharmacoeconomic evaluation alongside clinical trials has become an important research direction and the source of evidence. In order to facilitate the standardization of this research field, the current consensus focuses on the topic of how to conduct a pharmacoeconomic evaluation alongside clinical trials from the Chinese healthcare system and decision-making context. The consensus group reconciled expert opinions and developed recommendations covering the entire process of study design, data collection and management, data analysis, and methods and results reporting. A total of 24 recommendations regarding to methodology and practice were developed from eighteen aspects including target population, selection of comparators, calculation of sample size, data collection of healthcare resource utilization, data collection of health-related quality of life, cost analysis, health outcome analysis, addressing the missing and censored data, etc., with the aim to provide reference for scholars and decision makers in this research filed.