The eastern Junggar Basin, controlled by continental extension (rift), was deposited by lacustrine dominated sediments during middle Permian Lucaogou period. An unusual porphyritic-like texture was observed in Lucaogou/Pingdiquan dark fine-grained organic-rich sediments in two sub-tectonic units in the basin. The “phenocrysts” are composed of two types of mineral assemblages. The first is a coarse euhedral calcite assemblage in the Jimusar Sag, and the second consists of dolomite, analcime, and pyrite in the Shishugou Sag. The lithological and mineralogical features indicate a hydrothermal origin for these phenocryst-like minerals. The chondrite-normalized rare earth element patterns show flat or positive Ce anomalies and negative Eu anomalies, which reflect a suboxic to anoxic, off-axis site from the center of the fault system, where the temperature of the hydrothermal fluid might be less than 250 °C. The high ratios of BaN/LaN at 1.6–65.5, strongly positive Sr anomalies at Sr/Sr* = 5.54–39.9, and relatively low 87Sr/86Sr isotopes at 0.705002–0.705776 in the coarse calcite suggest an origin of mixed sources of lake water, underlying biogenetic sediments, and deep magmatic water. However, the low 87Sr/ 86Sr ratios of 0.705321–0.705968 in the dolomite and δ34SV-CDT of 10.8‰–12.3‰ in the pyrite indicate that water–underlying-rock interaction and the abiotic thermochemical sulfate reduction of lake water or organic matter might have participated together resulting in the precipitation of the dolomite–analcime–pyrite assemblages in the Shishugou Sag.