The Aqishan-Yamansu Fe-Cu-Au metallogenic belt in the Eastern Tianshan, NW China, hosts numerous Fe and Fe-Cu deposits that may have different genetic models, such as volcanic-hosted and skarn/IOCG types. These variations in genetic models are attributed to whether the mineralization is associated with hydrothermal activity related to volcanic or intrusive rocks. This study primarily focuses on garnets formed during the early skarn alteration in the Shuanglong Fe-Cu and Shaquanzi Fe deposits within this belt. Garnets from the Shuanglong deposit can be divided into two types and exhibit general homogeneity, with SL-Grt1 being Fe-rich and subsequently replaced by the Fe-poor SL-Grt2. Garnets from the Shaquanzi deposit display complex zonation patterns, SQZ-Grt1 show core–oscillatory zoned rim and SQZ-Grt2 show core–mantle–oscillatory zoned rim. Laser-ablation inductively coupled plasma-mass spectrometry (LA-ICP-MS) dating of SL-Grt1 and SL-Grt2 produced lower intercept 206Pb/238U ages ranging from 318.0 ± 6.4 Ma to 303.7 ± 16.4 Ma, coinciding with the multi-stage granite occurrence. In contrast, SQZ-Grt1 and SQZ-Grt2 yielded ages between 328.0 ± 2.6 Ma and 320.4 ± 1.7 Ma, corresponding to the timing of the hosted rhyolite. SL-Grt1 show light rare earth element (LREE) enrichment, and low concentrations of high field strength elements (HFSE), such as V and Zr, and appears to have formed rapidly within an open system. Conversely, SL-Grt2 is characterized by heavy rare earth element (HREE) enrichment and elevated HFSE contents, which could be formed slowly in a closed system. The variable composition in the SQZ-Grt1 and SQZ-Grt2 record cyclical changes in fluid kinetics (vigorous fluid flow vs. fluid stagnation). The cyclical zones in SQZ-Grt2 with HREE and HFSE concentrations below the detection limit indicate multiple inputs of external seawater. The distinct characteristics between Shuanglong and Shaquanzi garnets may reflect the difference between the single magma intrusion and complex volcanic activity. Combining previously published chronological data, this study elucidates a transition from the Middle Carboniferous volcanic-hosted Fe deposits (335–320 Ma) to the Late Carboniferous intrusion-related skarn or IOCG type Fe-Cu deposits (310–300 Ma) in the Aqishan-Yamansu belt.