This article presents results of the structural and morphological analysis of the fracture zones which are part of Doldrums Megatransform System (MTS), located in the northern part of the Equatorial Atlantic (6.5°–9° N) that include Vernadskiy and Bogdanov transform faults and the Doldrums and Pushcharovskiy megatransforms. Bathymetric map, based on the multibeam echo sounding data, collected during 45 cruise of the R/V Akademik Nikolaj Strakhov was used for this analysis. It was established that large-scale variations in the width of fracture zone valleys are determined by the distribution of stresses perpendicular to the fracture zone. In the areas with compressive stresses, the fracture zone valleys are narrower, and the in extension areas are wider. The difference in geodynamic settings within the MTS is due to the difference in spreading directions, which change from \(\perp \)89° to \(\perp \)93° when moving from south to north. The depth of fracture zone valleys consistently increases from the periphery of the MTS (Bogdanov and Doldrums faults) to the center (Pushcharovskiy fracture zone) in accordance with a decrease in the upper mantle temperature. In each fracture zone, the valley depth decreases from the rift- fracture zone intersections towards the center of the active part to a certain background depth. It is assumed that this phenomenon is the result of the uplift of the valley bottom, which occurred due to the decompaction of the lithosphere, caused by the serpentinization of ultramafic rocks. The violation of the revealed variations in the width and depth of fracture zone valley patterns occurs as a result of various ridges and uplifts formation in the fracture zone. In the axial zones of the active parts of the fracture zone valleys median ridges are widespread, extending parallel to the fracture zone and representing serpentinite diapirs squeezed out above the bottom surface. Transversal ridges which were formed 10‒11 million years ago as a result of the lithospheric plate edge flexural bending under extensional conditions are now located in the western passive parts on the southern sides of the of Doldrums and Pushcharovskiy fracture zone valleys. The transverse ridge on the northern side of the Vernadskiy fracture zone, which includes Mount Peyve, was formed between 3.65‒2.4 Ma. Due to the frequent jumps of the spreading axis in this region, it was divided into three segments. There are interfracture zone ridges in megatransforms, which in the active part consist of two fracture zone valleys. Time of their formation: in Pushcharovskiy megatransform ‒ 30‒32 million years ago and in Doldrums megatransform ‒ about 4 million years ago. Due to the curvilinearity of the outlines and under the pressure of moving lithospheric plates, the interfracture zone ridges experience longitudinal (along the fault) compressive and tensile stresses, which are compensated by vertical uplifts of their separate blocks and the formation of depressions, pull apart depressions, and spreading centers (the latter are only in Pushcharovskiy megatransform). Structure-forming processes that determine pattern and morphology of the fracture zones as a part of the MTS are related by their origin to the spreading and transform geodynamic systems.