The arid event that began in the Middle Jurassic Bathonian stage marks the second major drought event in northern China during the Jurassic period and had a profound impact on the development of modern terrestrial ecosystems. This study reconstructs the paleoclimate and paleoecosystem of the Middle Jurassic Santanghu Basin by analysing palynological assemblages and clay minerals from the Xishanyao and Toutunhe formations. The Xishanyao Formation contains a palynological assemblage of Cyathidites-Deltoidospora-Osmundacidites-Cycadopites (CDOC), which is assigned to the Aalenian-Bajocian. The Toutunhe Formation contains a Cyathidites-Classopollis-Quadraeculina (CCQ) assemblage, indicating a Bathonian age. In terms of vegetation types, during the Aalenian-Bajocian, the Santanghu Basin was dominated by ground cover vegetation primarily consisting of ferns, with a midstorey composed mainly of cycads/ginkgophytes, and a sparse canopy dominated by conifers. By the Bathonian, this shifted to a vegetation structure dominated by coniferous canopy vegetation, a subordinate midstorey of cycads/ginkgophytes, and a severely degraded ground cover dominated by ferns. Sporomorph EcoGroup (SEG) analysis indicates that the CDOC assemblage is characterised by high Lowland SEG wetter/drier and warmer/cooler ratios, reflecting a warm and humid climate. In contrast, the CCQ assemblage shows a low Lowland SEG wetter/drier ratio which indicates an arid climate. Clay mineral data reveal that the kaolinite content in the CCQ assemblage is significantly lower than in the CDOC assemblage. Evidence from both palynology and clay minerals suggests that the Santanghu Basin experienced a transition from a humid to a semi-arid climate near the Bajocian-Bathonian boundary in the Middle Jurassic.