As buildings move toward net-zero carbon targets, energy storage technologies are crucial in building-integrated photovoltaics (BIPV). Small-scale thermal storage systems can enhance traditional battery storage’s flexibility and total capacity, especially during heating and cooling seasons, while offering cost-control benefits. However, research on small-scale hybrid electrical and thermal storage systems in single buildings with high photovoltaic (PV) penetration remains limited. This paper proposes a novel configuration and control strategy for an integrated PV, electrical, and thermal storage system. A two-layer optimization model is developed based on historical energy consumption and PV generation data. The upper layer uses a multi-objective optimization approach that considers PV self-consumption, investment cost, and operational cost to optimize storage capacities. The lower layer designs a control strategy to minimize operational costs under time-of-use electricity pricing. A case study of a zero-energy office building in China’s cold climate zone shows that using battery storage alone (100 kWh) reduces operation costs by 40.24%. Incorporating thermal storage (70 kWh electrical, 80 kWh thermal) further reduces the costs by 11.45%. This study demonstrates the feasibility and cost-effectiveness of integrating thermal storage with battery systems in high-PV penetration buildings, providing a systematic framework for optimizing storage configurations and control strategies that improve PV self-consumption and lower costs in high-PV penetration scenarios.