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Continuous isotope labeling and tracing is often needed to study the transformation, movement, and allocation of carbon in plant-soil systems. However, existing labeling methods have numerous limitations. The present study introduces a new continuous labeling method using naturally 13C-depleted CO2. We theoretically proved that a stable level of 13C-CO2 abundance In a labeling chamber can be maintained by controlling the rate of CO2-free air injection and the rate of ambient airflow with coupling of automatic control of CO2 concentration using a CO2 analyzer. The theoretical results were tested and confirmed in a 54 day experiment in a plant growth chamber. This new continuous labeling method avoids the use of radioactive 14C or expensive 13C-enriched CO2 required by existing methods and therefore eliminates issues of radiation safety or unaffordable isotope cost, as well as creating new opportunities for short- or long-term labeling experiments under a controlled environment.