The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene) 2 ] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), esterterminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., H PI H (PI 0 )−pure PI (Hydrogen terminal), ω PI α1 (PI I ), ω PI α2 (PI II ), ω PI α3 (PI III ), ω PI α4 (PI IV ), ω PI α5 (PI V ), and ω PI α6 (PI VI ). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (R ee ), and radius of gyration (R g ). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2−α2, α4−α4, and α6−α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ω PI α2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]−[α2], [α4]−[α4], and [α6]−[α6] terminals in ω PI α2,α4,α6 melt systems is significantly stronger than in [ISO]−[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in H PI H and ω−ω, [α1]−[α1], [α3]−[α3], and [α5]− [α5] in ω PI α1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the H PI H , ω PI α1 , ω PI α3 , and ω PI α5 melt systems. Conversely, in the ω PI α2 , ω PI α4 , and ω PI α6 systems, we perceived stable clusters of [(α2) p ] [(α4) p ] and [(α6) p ] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.