The proper design of wave energy converters (WECs) is crucial for ensuring robustness in harsh wave climates without incurring the additional expense of unnecessary overdesign. The power take-off (PTO) mechanism, serving as a vital link between the moving body and the electric generator, is a key component in the design load analysis of WECs. However, the setting of PTO system parameters significantly impacts the dynamic behavior of the entire WEC system, leading to alterations in estimated loads. This work is dedicated to studying the influence of PTO control strategies on the identification of extreme loads of a heaving point absorber WEC. A nonlinear time-domain model is established to estimate the dynamic responses and loads of the WEC. Both PTO loads and end-stop loads under extreme conditions are examined, considering the wave climate of a realistic sea site. The results suggest that the PTO setting strategies significantly impact the extreme load exerted on both the PTO system and the end-stop system. Varying the PTO damping within a certain range could lead to a difference of 57% and 63% in short-term extreme loads for the PTO system and the end-stop system, respectively. Furthermore, the impacts of the PTO control strategy appear to be specific to each WEC component. The PTO parameters selected for reducing the extreme PTO loads might increase the extreme end-stop loads. A holistic examination is therefore recommended for estimating the extreme loads of WECs.