Environmental conditions, such as temperature, non-uniform irradiation, and solar shading, deeply affect the characteristics of photovoltaic (PV) modules in PV-assisted generation systems. Several local maximum power points (MPPs) are found in the power-voltage curve of PV systems constructed by series/parallel-connected PV modules under partially shaded conditions. The characteristics of PV systems change unpredictably when multiple MPPs occur, so the actual MPP tracking (MPPT) becomes a difficult task. Conventional MPPT methods for the PV systems under partially shaded conditions cannot quickly find the actual MPP such that the optimal utilization of PV systems cannot be achieved. Based on the p-n junction semiconductor theory, we develop a multipoint direct-estimation (MPDE) method to directly estimate the multiple MPPs of the PV systems under partially shaded conditions and to cope with the mentioned difficulties. Using the proposed MPDE method, the multiple MPPs of the PV systems under partially shaded conditions can be directly determined from their irradiated current-voltage and power-voltage characteristic curves. The performances of the proposed MPDE method are evaluated by examining the characteristics of multiple MPPs of PV systems with respect to different shading strengths and numbers of the shaded PV modules and also tested using the field data. The experimental results demonstrate that the proposed MPDE method can simply and accurately estimate the multiple MPPs of the PV systems under partially shaded conditions. The optimization of MPP control models and the MPPT for PV systems could be achieved promisingly by applying the proposed method.