Basin analysis is a research field to understand the formation and evolution of sedimentary basins. This task requires various geoscientific datasets as well as numerical and graphical modelling techniques to synthesize results dimensionally in time and space. For basin analysis and modelling in a comprehensive workflow, BasinVis 1.0 was released as a MATLAB-based program in 2016, and recently the software has been extended to BasinVis 2.0, with new functions and revised user-interface. As a case study, this work analyses the southern Vienna Basin and visualizes the sedimentation setting and subsidence evolution to introduce the basin modelling functions of BasinVis 2.0. This is a preliminary study for a basin-scale modelling of the Vienna Basin, together with our previous studies using BasinVis 1.0. In the study area, during the late Early Miocene, sedimentation and subsidence are significant along strike-slip and en-echelon listric normal faults. From the Middle Miocene onwards, however, subsidence decreases abruptly over the area and this situation continues until the Late Miocene. This is related to the development of the pull-apart system and corresponds to the episodic tectonic subsidence in strike-slip basins. The subsidence of the Middle Miocene is confined mainly to areas along the strike-slip faults, while, from the late Middle Miocene, the depocenter shifts to a depression along the N-S trending listric normal faults. This corresponds to the regional paleostress regime transitioning from NE-SW trending transtension to E-W trending extension. This study applies various functions and techniques to this case study, and the modelled results demonstrate that BasinVis 2.0 is effective and applicable to the basin modelling.