Dodder, a parasitic plant, obtains nutrients from its host through haustoria. The exchange of macromolecules between dodder and its host in nutrient-deficient environments is not well understood. In this study, it is shown that, when being subjected to nitrogen or phosphorus deficiency, at the transcript level soybean plants responded more strongly than did dodder plants. However, both plants exhibited significant changes at the protein level. Importantly, many different mRNAs and proteins were transported between soybean and dodder plant and the nutritional state of the soybean host strongly affected the interplant exchange of mRNAs and proteins, leading to variations in species and abundance of these macromolecules. This study provides evidence that transport of proteins between soybean and dodder is likely the major form of exchange of macromolecules. These findings shed new light on the interactions of dodder and its host during adaptation to nutrient deficiencies.