This dataset comprises the Chatvd19 age model and the microfacies analysis results of the Chatyr Kol Lake sedimentary composite profile. The composite profile relies on parallel piston cores, which were retrieved in 2012 with an UWITEC piston corer from the deepest part of the lake (~20m) (Kalanke et al., 2019). Analysis have been performed at the GFZ German Research Centre for Geosciences in Potsdam, Germany. The dataset "Age model and replicate varve counts of composite profile CHAT12 from Chatyr Kol Lake, Kyrgyzstan" contains the Age model with the composite depth, interpolated based varve thicknesses (column B), the age model and varve counting uncertainty estimates. The age model is based on the results of replicate varve counts, which were performed on overlapping large-scale petrographic thin sections along the whole composite profile from 63.0 to 623.5 cm depth. Thin section preparation followed the method described by Brauer and Casanova (2001) and included freeze-drying and vacuum impregnation of the sediment slabs with Araldite epoxy resin. Microfacies analysis was carried out on a Zeiss Axioplan microscope using different magnifications (25-400 x). The dataset "Microfacies analysis of thin sections including distribution of microfacies (varve) types and thicknesses, varve characteristics and semi-quantitative species abundances of composite profile CHAT12 from Chatyr Kol Lake, Kyrgyzstan" displays the results of the microfacies analysis, including the varve thicknesses, the distribution of observed microfacies (varve) types and thicknesses, the varve quality index and its distribution and the semi-quantitative analysis of species abundances. Species abundances were classified according to their low (=1), middle (=2) and high (=3) abundances. The dataset "Varve thickness measurements of discontinuous varves between 63.0 and 41.9 cm composite depth of composite profile CHAT12 from Chatyr Kol Lake, Kyrgyzstan" displays varve thickness measurements of discontinuous varves between 63.0 and 41.0 cm composite depth, which were i.a. used for interpolation of the upper homogenous sediments (0-63.0 cm depth).