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Physiological integration facilitates clonal plants to deal with heterogeneous resources. However, little is known about how nutrient patchiness affects its use and stoichiometry in clonal plants. We conducted an experiment with Cynodon dactylon, Glechoma longituba, and Potentilla reptans to address the effects of physiological integration on nutrient use efficiency and N:P ratios. For C. dactylon, the effects of nutrient patchiness on N use efficiency (NUE), P use efficiency (PUE), and N:P ratio were stronger in daughter ramets than in parent ramets; for G. longituba, nutrient patchiness affected PUE and N:P ratio of parent and daughter ramets, but not NUE; for P. reptans, nutrient patchiness decreased NUE, PUE, and N:P ratio, regardless of parent or daughter ramets. PUE was associated with N:P ratios in three clonal plants and this association of NUE with N:P ratios varied with species. Our findings suggest that physiological integration alters nutrient use efficiency and N:P ratios of clonal plants under patchy nutrients and that these effects are linked to clonal species identity.