Two-dimensional (2D) materials based on molybdenum sulfide (MoS2) have shown promising applications in semiconductors, optoelectronics, and catalysis. The variety of applications implies a controlled manipulation of purity, shape, and phase of such materials. This work elaborates on the structural characterization of MoS2 micro-assemblies produced in a chemical vapor deposition (CVD) system with emphasis on the pyramidal structures formed at high temperature and low gas rate, on a silicon dioxide (SiO2) substrate. A precise control of temperature and gas rate in the CVD process prompts the growth of pyramidal and other micron-size arrangements of MoS2 layers. An integrative set of high-resolution and analytical electron microscopy techniques, in conjunction with Raman and X-ray photoelectron spectroscopy (XPS), revealed the structural features of the MoS2 microstructures. Raman and XPS confirmed the presence of MoS2 and some residual oxide phases. Ultra-high-resolution scanning electron microscopy provided direct observation of the distinctive stacking of layers forming the pyramidal microstructures. Cross section samples from selected structures were done using focused ion beam. An extent of transmission electron microscopy and Cs-corrected scanning transmission electron microscopy (Cs-corrected STEM) results is discussed. This approach allowed to understand the growth mechanism of the triangular MoS2 microstructures through spiral grow around a screw dislocation, initiated at the center of the assembly.