The PGE-Cu-Ni Oktyabr’sky deposit, related to the Kharaelakh intrusion, contains the largest sulfide ore bodies in the world. Various models have been proposed to explain its formation based on the mineralogical and textural characteristics of the sulfide ores. However, the underlying structure of the intrusion, critical to understanding the deposit’s formation, has not been well studied until now. For the first time a 3D model of the center deposit with C-3 and C-4 orebodies representing its main part has been created. The model reveals that the intrusion in this area is a thin plate, rather than a tubular or honolithic body, as previously assumed. This morphology does not support the idea of ore formation by in situ reaction between primary magma and host rocks. Instead, sulfides were transported by magma from a deeper zone in the chamber. Within this area, two pulses of magma were identified, forming the Northern and Southern intrusive branches. They are similar in inner structure; however, some differences exist. The rocks of these intrusions are identical in terms of their major components but differ in metals (Cu/Ni ratios, Co, Zn, and V contents), which is particularly reflected in the composition of the chalcopyrite group of minerals. The picritic gabbro-dolerites presented in both intrusive bodies crystallized under similar conditions, namely, T and fO2, with an accuracy of the applied methods (±15 °C and ± 0.4 lgfO₂, respectively) from two portions of magma that differ from those of the taxitic gabbro-dolerites. Therefore, the Oktyabr’sky deposit has a more complex structure in its central part than has been previously reported. Considering earlier published data from the western and eastern parts, it can be concluded that the Karaelakh intrusion consists of several intrusive bodies rather than a single large massif that should be consider in future models.