Soil organic matter (SOM) plays pivotal roles in characterizing dryland structure and function; however, remotely sensed spatially-detailed SOM mapping in these regions remains a challenge. Various digital soil mapping approaches based on either single-period remote sensing or spectral indices in other ecosystems usually produce inaccurate, poorly constrained estimates of dryland SOM. Here, a framework for spatially-detailed SOM mapping was proposed based on cross-wavelet transform (XWT) that exploits ecologically meaningful features from intra-annual fractional vegetation and soil-related endmember records. In this framework, paired green vegetation (GV) and soil-related endmembers (i.e., dark surface (DA), saline land (SA), sand land (SL)) sequences were adopted to extract 30 XWT features in temporally and spatially continuous domains of cross-wavelet spectrum. We then selected representative features as exploratory covariates for SOM mapping, integrated with four state-of-the-art machine learning approaches, i.e., ridge regression (RR), least squares-support vector machines (LS-SVM), random forests (RF), and gradient boosted regression trees (GBRT). The results reported that SOM maps from 13 coupled filtered XWT features and four machine learning approaches were consistent with soil-landscape knowledge, as evidenced by a spatially-detailed gradient from oasis to barren. This framework also presented more accurate and reliable results than arithmetically averaged features of intra-annual endmembers and existing datasets. Among the four approaches, both RF and GBRT were more appropriate in the XWT-based framework, showing superior accuracy, robustness, and lower uncertainty. The XWT synthetically characterized soil fertility from the consecutive structure of intra-annual vegetation and soil-related endmember sequences. Therefore, the proposed framework improved the understanding of SOM and land degradation neutrality, potentially leading to more sustainable management of dryland systems.