This paper presents the modeling of a photovoltaic system under complex shading conditions. The approach integrates a complete PV array with each cell modeled separately including shadow coefficients depending on a percentage of area impacted and the level of irradiance (named shaded opacity). A dedicated global maximum power point tracking algorithm is developed taking into account all behavior of the system, in particular, under compound shading conditions. The Hybrid Bond-Graph tool is chosen to facilitate the modeling of the energy flows of the inner of PV cell, between the cells, panels and boost converters in the aim of future work in complex micro-grid and energy conversion.