Maintaining species richness and conserving endemic or rare species in dune areas has been a research focus in recent years. However, few reports can be found on how dune stabilization affects species composition in the interdune wetland. This paper is to elucidate how dune stabilization in the northeastern Inner Mongolia of China is linked to plant diversity in the interdune wetland of different sizes. We selected 11 interdune wetlands of different sizes in both stabilized and active dunes, respectively. The change in species richness between the active and stabilized dunes was compared. Total species number in the interdune wetland increased logarithmically with the enlargement of wetland area for both stabilized and active dunes. However, when the area was the same, species number in stabilized dunes was 15 more than that in active dunes. Pioneer species number in interdune wetlands increased with the increase in wetland area for both stabilized and active dunes, but not statistically significant. However, when the area was the same, species number in stabilized dunes was slightly 1 fewer than that in active dunes. Artemisia wudanica, an endemic pioneering dune semishrub, was found in 9 of 11 investigated interdune wetlands of active dunes, but did not occur in 11 investigated interdune wetlands of stabilized dunes. We concluded dune stabilization in the northeastern Inner Mongolia, on one hand, raises species richness, and on the other, leads to the loss of endemic or rare pioneer species in interdune wetlands.