The aim of this work is to identify main impact factors affecting variations in the geomorphology of the Mariana Trench which is the deepest place of the Earth, located in the west Pacific Ocean: steepness angle and structure of the sediment compression. The Mariana Trench presents a complex ecosystem with highly interconnected factors: geology (sediment thickness and tectonics including four plates that Mariana trench crosses: Philippine, Pacific, Mariana, Caroline), bathymetry (coordinates, slope angle, depth values in the observation points). To study such a complex system, an objective method combining various approaches (statistics, R, GIS, descriptive analysis and graphical plotting) was performed. Methodology of the research includes following clusters: R programming language for writing codes, statistical analysis, mathematical algorithms for data processing, analysis and visualizing diagrams, GIS for digitizing bathymetric profiles and spatial analysis. The statistical analysis of the data taken from the bathymetric profiles was applied to environmental factors, i.e. coordinates, depths, geological properties sediment thickness, slope angles, etc. Finally, factor analysis was performed by R libraries to analyze impact factors of the Mariana Trench ecosystem. Euler-Venn logical diagrams highlighted similarities between four tectonic plates and environmental factors. The results revealed distinct correlations between the environmental factors (sediment thickness, slope steepness, depth values by observation points, geographic location of the profiles) affecting Mariana Trench morphology. The research demonstrated that coding on R language provides a powerful and highly effective statistical tools, mathematical algorithms of factor analysis to study ocean trench formation.