Water conservation is an essential indicator of the hydrological regulation capacity of terrestrial ecosystems. At the regional scale, the water conservation capacity of an ecosystem is typically assessed using the water balance model (WBM). However, the estimation of the runoff depth relies heavily on rainfall data and the ecosystem runoff coefficient look-up table, which introduces uncertainties in the assessment results. To address this issue, this study constructed a new method for quantifying the spatiotemporal distribution pattern of runoff depth based on the ecosystem type and regional spatial heterogeneity characteristics using runoff observation data from hydrological observation stations. We use this new method to evaluate the water conservation capacity of the ecosystem on a regional scale and compare and analyze the differences between the new and old methods in terms of connotation, data format, and evaluation results. Finally, we discuss the advantages and potential applications of the new method.