The agro-pastoral transitional zone (APTZ) in Northern China is one of the most important ecological barriers of the world. The commonly-used method to identify the spatial distribution of ATPZ is to apply a threshold rule on climatic or land use indicators. This approach is highly subjective, and the quantity standards vary among the studies. In this study, we adopted the spatial continuous wavelet transform (SCWT) technique to detect the spatial fluctuation in normalized difference vegetation index (NDVI) sequences, and as such identify the APTZ. To carry out this analysis, the Moderate Resolution Imaging Spectroradiometer (MODIS) NDVI 1-month data (MODND1M) covering the period 2006–2015 were used. Based on the spatial variation in NDVI, we identified two sub-regions within the APTZ. The temporal change of APTZ showed that although vegetation spatial pattern changed annually, certain areas appeared to be stable, while others showed higher sensitivity to environmental variance. Through correlation analysis between the dynamics of APTZ and precipitation, we found that the mean center of the APTZ moved toward the southeast during dry years and toward the northwest during humid years. By comparing the APTZ spatial pattern obtained in the present study with the outcome following the traditional approach based on mean annual precipitation data, it can be concluded that our study provides a reliable basis to advance the methodological framework to identify accurately transitional zones. The identification framework is of high importance to support decision-making in land use management in Northern China as well as other similar regions around the world.