A cross-sea bridge under construction was considered as an example. The thermal stress and its influencing factors of the prefabricated bridge pier during connection with the cast-in-place cap were analyzed through numerical simulation. Crack control measures were proposed and field tests were conducted combined with the offshore construction conditions. Results show that the main factor causing thermal stress is the thermal expansion of the core-filled concrete, and the secondary factor is the temperature gradient of the pier. The maximum tensile stress increases by 15.4% when the concrete pouring temperature is increased from 10 °C to 40 °C. The control effect of setting the thermal insulation buffer layer is the best as a single measure, followed by the cooling water pipes, optimization of concrete proportion, layered construction and stress dissipation hole. The effect of outer insulation and inner cavity ventilation is poor. The recommended strategy includes optimizing concrete proportion and pouring concrete in three layers, in which the first layer and the second layer are respectively provided with a thermal insulation buffer layer and a stress dissipation hole. The results of field tests verify the effectiveness of the recommended strategy for crack suppression.