Mostly used in the early stage of oil exploration, three-dimensional stratigraphic models help subsurface data interpretation, evaluation and understanding of complex interactions of sedimentary depositional systems. These models give quantitative information about geometry, continuity, location and dimensions of sedimentary units and also characterize their sedimentary facies. This paper suggests an approach based on sequence stratigraphy concepts, which interpret transgressive/regressive shifts, the timing of all system tract and sequence boundaries (e.g. maximum flooding surface, correlative conformity, or conformable transgressive surface) as the interplay of sedimentation and base-level fluctuations. The presented model integrates well data, seismic survey and geologic knowledge to model sedimentary units architecture, sequence boundaries geometry and facies proportions in three dimensions. This solution simplifies the initial problem by modeling singly the geometry in the geological space (x,y,z) and the properties in the geochronological space (u,v,t). A forward model accounting for well data and geological knowledge is computed in the geochronological space where isochroneous surfaces are strictly horizontal. A quality control of the sequence boundaries geometry is done in the geological space in order to fit to the seismic reflector. After the quality control, properties (facies, sand/shale ratio, depositional water depth, ...) are painted from the geochronological space to the geological space. Last, by modeling the sedimentary units in time layers, this approach opens some doors to complex geostatistical analyses such as compositional trends in sediments.