Hevea brasiliensis is an important natural rubber-producing plant. Rubber particles (RP) in latex are important organelles for the synthesis of natural rubber, which can be divided into large rubber particles (LRP) and small rubber particles (SRP) according to the diameter. Although the specific mechanism of its regulation of natural rubber synthesis in response to exogenous ethylene stimulation has been studied. However, the specific regulatory mechanism of LRP and SRP in regulating natural rubber synthesis in response to ethylene stimulation is still unclear. In order to clarify the role of RP with different diameters in the synthesis of natural rubber, LRP and SRP stimulated by ethylene were isolated and the proteins of corresponding samples were extracted for differential protein analysis. 37 differential proteins in response to ethylene stimulation were identified in the LRP, which were involved in natural rubber biosynthesis, glycolysis/gluconeogenesis, carbon metabolism and amino acid biosynthesis, and some other metabolic pathways, including four members of the REF/SRPP family. 56 differential proteins were identified in SRP, which were involved in protein processing, endocytosis, splicing in endoplasmic reticulum, and some other metabolic pathways, including five members of the REF/SRPP family. The key differential accumulation protein REF138 had many isoforms with different isoelectric points (pI) and molecular weights (MW). REF138 isoforms below the standard pI (4.80) on LRP were down-regulated in response to ethylene stimulation, while isoforms above the standard pI were up-regulated to ethylene stimulation. Different from LRP, more isoforms of REF138 on SRP changed in response to ethylene stimulation, and isoforms with standard MW (14.7 kDa) were up-regulated in response to ethylene stimulation, while isoforms with higher than standard MW were down-regulated in response to ethylene stimulation. The function analysis of key differential proteins showed that there were interactions among the members of the REF/SRPP family. REF138, REF175, REF258, SRPP117 and SRPP204 may form protein complexes and bind to RP. In addition to the members of the REF/SRPP family, 20 proteins interacting with REF138 were mainly involved in the spliceosome and endocytic metabolic pathways, and 50 proteins interacting with REF258 were involved in the regulation of lipid metabolism and the synthesis of secondary metabolites. In conclusion, functional analysis of differential proteins and the interaction proteins responsive to ethylene stimulation on LRP and SRP might preliminarily reveal the metabolic regulatory mechanism of LRP and SRP in regulating natural rubber synthesis in response to exogenous ethylene stimulation.