Focusing on the research scenario that integrates value-based healthcare objectives with the pharmaceutical group purchasing model, this study delineates value-based healthcare objectives in pharmaceutical group purchasing from three perspectives: drug sales price, drug quality, and service level. We construct a three-level pharmaceutical group purchasing supply chain consisting of drug manufacturers, medical institutions, and non-profit drug group purchasing organisations. Under centralised and decentralised decision-making, we introduce cost-sharing contracts and “cost-sharing-quantity-discount” contracts to analyse the impact of factors such as drug sales price, quality, and sensitivity of the service level. The study found that: (1) Compared with centralised decision-making, the optimal drug quality and service level in decentralised decision-making and the optimal profits of drug manufacturers and medical institutions will decrease. However, the optimal drug sales price in decentralised decision-making always deviates from that in centralised decision-making, leading to higher or lower drug sales prices. (2) The incorporation of value-based healthcare objectives in the pharmaceutical group purchasing through cost-sharing contracts depends on changes in the proportion of drug quality costs borne by medical institutions. If the proportion is too high, medical institutions will suffer greater losses because they bear too much of the cost. (3) Under certain conditions, cost-sharing contracts can improve supply chain efficiency but cannot achieve supply chain coordination, while the combination of “cost-sharing-quantity-discount” contracts can achieve supply chain coordination in pharmaceutical group purchasing.