Desert strata consist of dune and interdune deposits, and they have different magnetic properties. Contrasting magnetic properties of these two types of strata is a foundation for extracting paleoclimate information from dune-interdune strata in these eco-fragile regions, but few have done so. Here we compared magnetic properties between dune and interdune strata from the late Miocene desert deposits in the northwestern Tarim Basin. We found that interdune strata displayed enhanced magnetic properties mainly due to content increase of stable single-domain (SSD) and small pseudo single-domain magnetite (PSD) within chlorite layers. But magnetic enhancement in interdune strata does not correspond with content increase of superparamagnetic (SP) ferrimagnetic minerals. Our high-resolution transmission electron microscope results suggest pedogenic SSD and small PSD magnetite form within chlorite layers, and we propose weathering of chlorites resulted in high concentration of Fe (II) and Fe (III) ions within layers, facilitating the formation of SSD and small PSD magnetite. By contrast, dry climate in the Tarim Basin results in micropore spaces between mineral particles having limited concentration of Fe (II) and Fe (III) ions, inhibiting SP magnetite formation. This pattern is different from Chinese loess-paleosols sequence, where magnetic enhancement is accompanied with content increase of both SP and SSD or small PSD ferrimagnetic mineral content. Therefore, magnetic enhancement pattern differences (whether magnetic enhancement is accompanied with SP magnetite formation) may inform climate conditions. To infer environmental variations in arid regions using magnetic parameters, reliance on proxies that indicate the relative content of ferrimagnetic grains or content of magnetic grains with stable remanence is essential.