A coupled pollen-brGDGT paleoclimate reconstruction approach has been tested to provide independent and robust estimates of Holocene climate and environment changes in the extremely arid environment of the mountainous areas ranging from northern Arid Central Asia (ACA) to the Mongolian Plateau. The two proxies were calibrated for both global and local modern data sets (NMSDB). This multi-proxy approach was then applied to a sediment core collected from Lake Ayrag, Arkhangai, covering the Late Holocene. In addition to brGDGTs and pollen, we also performed magnetic susceptibility, micro-XRF, elemental and isotopic bulk chemistry, and Non-Pollen Palynomorph (NPP) analyses on the Lake Ayrag sediments in order to better understand the lake system and human impact dynamics. While the globally calibrated record (both for pollen and brGDGTs) displayed a slight millennial-scale cooling, the locally calibrated results exhibit centennial-scale climate oscillations such as the 4.2 and 3.5 kyr events, the Roman Warm Period (RWP), Dark Ages Cold Period (DACP), Medieval Warm Period (MWP) and Little Ice Age (LIA). These climate oscillations and vegetation changes are discussed with regard to the main Mongolian human historical occupation events documented by pastoralism proxies, especially the Xiongnu, Mongol Empire, Mandchou and Soviet periods. The climate systems currently dominating the Mongolian Plateau are difficult to resolve because inter-annual climate variability is pronounced. However, precipitation mainly occurs in summer (easterly monsoon driven) when the winter Westerlies lead the air mass movement. In the past, both pollen and biomarkers exhibited anti-correlated trends with annual precipitation and temperature: over the last 4000 kcal yr BP, the warm periods (MWP, RWP) were dry and the cold periods (LIA, DACP, 3.5 kyrs) were humid. Thus, the East Asian Summer Monsoon (i.e., warm and wet conditions dominant during summer) seems not to have influenced central Mongolian climate during the Late Holocene, which could have remained dominated by the Westerlies/Siberian High cells conflict. A comparison between the Ayrag record and other paleoclimate records from the Baikal area (Dulikha), Mongolian Plateau (D3L6, D1L1, NRX, ATM), and continental China (Kesang, Baluk and Tonnel caves, XRD section) to the Loess Plateau (Huangye and Xianglong caves) suggests that the monsoon front has oscillated since the Early Holocene. A climate synthesis following strictly the same approach (locally calibrated brGDGTs vs. pollen-inferred climate) for all the ACA records available for the Late Holocene helps us to resolve the climate systems paced by centennial to millennial-scale oscillations and their consequences for human societies.