The response of nitrogen cycling in lake systems to icehouse-to-greenhouse climate transitions remains essentially uninvestigated, even though similar responses are imminent in modern lakes. Here, we examine the biogeochemical nitrogen cycle in Paleolake Junggar, a saline lacustrine system in the Jimsar Sag (Junggar Basin, NW China) through analysis of elemental, isotopic, and biomarker proxies in the Middle Permian Lucaogou Formation. The study section comprises three depositional intervals (Intervals A, B, and C) based on variations in organic matter abundance and lithofacies associations. Our results document a climatic shift from cold-arid in Interval A (oldest) to warm-humid conditions in Interval C (youngest), promoting terrestrial nutrient influx. Salinity and redox proxies suggest higher salinity and stronger anoxia in Intervals A and C compared to Interval B. Biomarkers show an abundance of halotolerant green algae in Interval A, with increased cyanobacterial inputs in Intervals BC. A decrease in nitrogen isotopic compositions (delta N-15) records a climate-driven reduction in lake water pH, defining three biogeochemical nitrogen cycling stages. Under the initially arid climate conditions of Interval A, anoxic and alkaline conditions were favorable to halotolerant green algae and methanogens, and ammonia volatilization was strong (delta N-15 > +10 parts per thousand). Climate warming and increased chemical weathering in Interval B led to cyanobacterial blooms in a nutrient-rich watermass along with incomplete denitrification accompanied by possible biological nitrogen fixation (+8 parts per thousand < delta N-15 < +10 parts per thousand). Following development of a wetter climate in Interval C, the stratified and neutral-pH lake was marked by increased productivity and bottom-water anoxia, facilitating the enrichment of organic matter and triggering a shift to dominance of denitrification (+5 parts per thousand < delta N-15 < +8 parts per thousand). These findings demonstrate that nitrogen isotopes can serve as an effective proxy for climate change in alkaline lakes, especially offering insights into the response of biotic community structures to Middle Permian climate warming.