Primary macronutrients nitrate (N), inorganic phosphate (Pi), and potassium (K) are major elements to build-up fundamental biomolecules, function in energy transfer and the regulation of enzyme activity in plants. In response to the limited macronutrient availability in soil, plants display a high degree of adaptive responses, depending on both local and systemic regulation networks to coordinate nutrient homeostasis within the whole plant. There are several types of molecules such as metabolites, peptides, proteins, and RNAs are known to be involved in the transduction of systemic signaling. However, the roles of the proteins in systemic regulating different types of nutrient deficient stress are still elusive. In this study, the mobile proteins were collected from the phloem sap of heterografted plants under different nutrient stresses and quantitated by the isobaric labeling approach. Among 3200-3700 quantified cucumber and watermelon proteins in the phloem sap of heterografted cucumber/watermelon, 675, 785, and 796 cucumber proteins were found to be systemically translocated under N, Pi, and K deficiency, respectively. Those long-distance translocated cucumber proteins with more than 1.3- or less than the 0.76-fold change in abundance could be involved in carbohydrate metabolic process, molecular biosynthetic process, ubiquitin/protein degradation, and cytokinesis. Interestingly, some potential RNA-binding proteins could be long-distance trafficking in response to N, Pi, or K-deficiency. For instance, one of cucumber protein which is the homolog of one Arabidopsis heterogeneous nuclear ribonucleoprotein showed reduced abundance upon Pi-deficiency in the root-to-scion direction, supporting its potential role as a negative regulator in salt and osmosis stress responses. These mobile proteins with the change in relative quantities in response to N, Pi, or K deficiency should provide a better understanding of the mobile signaling mechanisms and homeostasis for nutrient starvation.