Germanium, a critical metal, is predominantly located in lignite and lead–zinc ore. The germanium was commonly extracted from the fly ash of germanium-rich lignite (GRL), however, facing the challenges of specific combustion conditions, low lignite’s thermal efficiency and value, high CO2 emissions, and waste acid treatment. Therefore, in this work, a novel method for directly leaching germanium from the GRL was proposed, facilitating low-carbon extraction under mild conditions, and reducing lignite loss during leaching process. Results showed that leaching germanium from the GRL using thionyl chloride achieved the goals of “kill two birds with one stone”, i.e., leaching efficiency of germanium above 95 wt% and recovery yield of lignite over 95 wt%. Specifically, the theoretical leaching efficiency of germanium reached 99.60 wt% while the recovery yield of lignite reached 86.35 wt%, at the temperature of 20 °C, liquid–solid ratio of 4 mL/g, and leaching time of 6 h. Most of the leached germanium was remained in the aqueous phase after the leaching solution was quenched, facilitating the subsequent separation of germanium. In this study, efficient extraction of germanium from the GRL was achieved with a high recovery yield of lignite, preserving the matrix structure and main composition of lignite. Therefore, this method provides a feasible way for efficient extraction of germanium from lignite with low-carbon emission under mild condition.