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The special and representative polymorphous pyrites of the Logatchev area, Mid-Atlantic Ridge, have a close evolution relationship. There are relatively complete pyrite intermediates undergoing a series of evolutions from disordered nano-micron crystals → framboids → colloidal and subhedral structures. This study focuses on a sulfide-bearing tuff sample of the Logatchev area and presents the detailed mineralogical, textural and geochemical results of a series of intermediate products, from pyrite framboids to subhedral crystals, using results from secondary ion mass spectrometry, field emission scanning electron microscopy, electron backscattered diffraction, and electron microprobes. Framboids packed with nanocrystals are significantly with negative δ34S (−28.3 to −17.4‰), probably formed via organoclastic sulfate reduction (OSR) in the seawater column or shallow marine sediment. And their associated microcrystal framboids have less-negative δ34S value (−22.3 to −8.8‰) and high Cu/Zn ratio, which are interpreted as framboids continuous growth by venting fluids with high temperature in an open system. During the diagenetic stage, the evolution of framboidal pyrites to subhedral crystals occurs mainly through two ways: cementation and rearrangement after growth. As an intermediate, the δ34S values of cemented framboids (−7.6 to +8.7‰) are close to the colloidal and subhedral structure pyrites (+9.1 to +11.2‰), reflecting the subsequent precipitation of pyrite and secondary overgrowth in a closed environment after burial. During the recrystallization process from nano-micron crystals to cemented framboids to colloidal or subhedral structures, the decreasing trend of SiO2 contents (come from the surrounding basement) and increasing Fe, S, Mo contents revealed the consequence of continuous expulsion of silicate in the intergranular pore space, which provides evidence for framboids aggregated and evolving to euhedral pyrite. Some intermediates from framboids to massive pyrites have a certain local ordering. Regulated by surface energy, grains in some framboidal pyrites are physically rotated and repositioned during the growth process, which show either 〈1 0 0〉 or 〈1 1 1〉 preferred orientations. The planes with higher energy are combined to form a regular arrangement and assembled into a polygonal frame until it evolves into a subhedral structure. The size uniformity of grains derived from framboidal pyrite is key to aggregation and self-organization. The research results are helpful for understanding the genesis mechanism of framboidal pyrite and its evolution process to a euhedral structure, which is of great significance to explore the structural growth of pyrite aggregates and the changes in the environmental response.