Strontium (Sr) and neodymium (Nd) isotopic compositions enable identification of dust sources and reconstruction of atmospheric dispersal pathways. The Sr and Nd isotopic compositions in eolian dust change systematically with grain size in ways not yet fully understood. This study demonstrates the grain size effect on the Sr and Nd isotopic compositions in loess and 2006 dust fall, based on analyses of seven separated grain size fractions. The analytical results indicate that Sr isotopic ratios strongly depend on the grain size fractions in samples from all types of eolian dust. In contrast, the Nd isotopic ratios exhibit little variation in loess, although they vary significantly with grain size in samples from a 2006 dust fall. Furthermore, Nd model ages tend to increase with increasing grain size in samples from all types of eolian dust. Comparatively, Sr isotopic compositions exhibit high sensitively to wind sorting, while Nd isotopic compositions show greater sensitively to dust origin. The principal cause for the different patterns of Sr and Nd isotopic composition variability with grain size appears related to the different geochemical behaviors between rubidium (Rb) and Sr, and the similar geochemical behaviors between samarium (Sm) and Nd. The Nd isotope data indicate that the various grain size fractions in loess have similar origins for each sample. In contrast, various provenance components may separate into different grain size fractions for the studied 2006 dust fall. The Sr and Nd isotope compositions further confirm that the 2006 dust fall and Pleistocene loess in Beijing have different sources. The loess deposits found in Beijing and those found on the Chinese Loess Plateau also derive from different sources. Variations between Sr and Nd isotopic compositions and Nd model ages with grain size need to be considered when directly comparing analyses of eolian dust of different grain size.