Reconstructions of global surface temperature, dominated by records from the northern extratropics, show an apparent Holocene cooling trend after the early Holocene Climatic Optimum. However, model simulations suggest a global warming Holocene tendency. This “Holocene temperature conundrum” may be caused by the seasonal bias of paleotemperature proxies. Here we report a quantitative Holocene record with ~100-year resolution based on branched glycerol dialkyl glycerol tetraethers (brGDGTs) from an alpine lake in southwestern China. Our reconstructed Holocene temperature record displays a steady long-term trend without distinct cooling or warming changes. Based on the temperature values and their evolution over time, our reconstruction is interpreted to present temperature changes in ice-free seasons from March to November. Unlike the often-documented Holocene cooling of regional summer temperatures driven by boreal summer insolation, this observed trend in our reconstructed temperatures is probably caused by slightly decreasing local ice-free season insolation and somewhat compensated by increasing atmospheric greenhouse gas concentrations. Our results demonstrate that the climatic drivers of ice-free season and summer temperature changes could be different and highlight the significance of elucidating the seasonality of proxies before using them for paleoclimate reconstructions.