A business to business (B2B) e-marketplace is an Internet-based inter-organizational system that facilitates online businesses. It provides two basic functions: search and transaction. Accordingly, organizational usage of B2B e-marketplaces varies across these two functions. The previous research mainly applies the Diffusion of Innovation (DOI) theory to predict the usage of B2B e-marketplaces, but this theory is insufficient in explaining the unbalanced usage of search versus transaction. This research attempts to fill this gap. We identify a cognitive limitation associated with each usage, i.e., insufficient knowledge of B2B e-marketplaces corresponds to the usage of search and incapability of foreseeing all consequences corresponds to the usage of transaction. Then, we incorporate perceived institutional norm and organizational trust as two remedies into the DOI theory, and argue that the former will affect the use of B2B e-marketplaces for search while the latter will affect the usage of transaction. A field survey is conducted to collect the data, and structural equation modeling is employed to test the research model. The results confirm the hypotheses. Besides, relative advantage and perceived compatibility from the DOI theory also affect both types of usage. This research implies that the usage of Internet-based inter-organizational systems may encounter cognitive limitations, and highlights how the DOI theory can be extended to account for the usage of information systems that provide multiple uses at different adoption stages.