The relationship between the thrombolitic mesostructures and their depositional environments is still poorly understood due to inconsistent results by sedimentary investigation. Rare earth elements plus yttrium (REY) in ancient microbialites have been extensively applied to paleoenvironmental studies owing to their fractionation in different depositional environments. In order to investigate the environmental controls on thrombolitic mesostructures, we present the REY concentrations and patterns of four types of mesostructures of the Miaolingian (Cambrian) thrombolites in the Changhia Formation at the Jiulongshan section, Shandong Province, China. The REY compositions of those thrombolites show two distinctive groups: (1) light REY depleted patterns with negative Ce anomalies in spotted (SM) and layered mesostructures (LM) of thrombolites; and (2) flat patterns with weak Ce anomalies in dendritic (DM) and meshed mesostructures (MM) of thrombolites. Controlling factors analysis reveals that terrigenous detritus inputs have stronger influence on REY in SM and LM. In contrast, early diagenetic porewaters from underlying sediments have more serious impacts on REY concentrations and patterns in DM and MM. Our results clearly indicate that SM and LM were formed under oxic marine settings with minor terrigenous inputs, whereas DM and MM formed under suboxic marine settings suffered from early diagenetic porewater from underlying sediments. This new geochemical evidence suggests that thrombolitic mesostructures were strongly influenced by paleoenvironment, and REY of thrombolites with controlling factors analysis can be utilized as effective proxies for paleoenvironments.