The uplift history of the Tibetan Plateau (TP) remains uncertain despite many scientific studies. The development of a novel paleoaltimeter may provide a crucial tool for addressing this issue. H-shaped glycerol dialkyl glycerol tetraethers (H-GDGTs) are analogs of GDGTs and considered to have potential in paleotemperature reconstructions, becoming, in turn, a potential indicator of paleoaltitude. This study analyzed the H-GDGTs in Late Miocene sediments from the Mojiazhuang (MJZ) Section in the Xining Basin (XB) and evaluated the potential of these less-explored biomarkers in paleotemperature and paleoaltitude reconstructions. Only branched H-GDGTs (H-brGDGTs) were detected; their relative abundance in relation to brGDGTs (%H-brGDGTs) exhibited a strong correlation with proxy-based palaeotemperature. However, their exceptionally elevated values necessarily impose limitations on the feasibility of quantitatively reconstructing paleotemperatures based on %H-brGDGTs, rendering them suitable solely as a qualitative temperature indicator. The methylation index of H-brGDGTs (H-MBTacyclic) can be effectively used to quantitatively reconstruct paleotemperatures. The challenge H-MBTacyclic poses is its potentially limited use for lower temperatures, as it may exhibit incomplete detection of H-brGDGT components. These provisos being the case, both %H-brGDGTs and H-MBTacyclic were nonetheless effectively used to document the cooling and TP uplift event in the XB during the ∼10.5–8 Ma period, aligning with the reconstruction based on brGDGTs. The quantitative paleoaltitude reconstruction using H-MBTacyclic values indicated an uplift amplitude of ∼1 km. As an independent proxy of paleotemperature and paleoaltitude, H-brGDGTs once again would appear to underscore the presence and significance of this Late Miocene uplift event. Given the challenges encountered when using H-brGDGT-based proxies, further investigations into modern samples and evaluations of deep-time samples are imperative for any future application.