Based on a two-tier supply chain system consisting of “technology-based manufacturers and retailers”, this study constructs game-theoretic models under three policies: no subsidy, price subsidies for consumers, and research and development (R&D) subsidies for manufacturers. It explore the government’s choice of subsidy strategies for technology-based firm supply chain under demand disturbances. The findings indicate that when the demand disturbance amplitude is large, both subsidy strategies can effectively incentivize manufacturers to enhance R&D efforts. However, when the demand disturbance amplitude is small, the price subsidy strategy becomes ineffective. When the demand disturbance amplitude is large, the price subsidy strategy maximizes manufacturers’ profits, while the R&D subsidy strategy is more beneficial to retailers’ profits and consumer surplus. When the demand disturbance amplitude is small, both subsidy strategies only increase manufacturers’ profits and do not affect the retailers’ profit or consumer surplus.