Terminal phospholipid groups contribute considerably to the excellent comprehensive properties of NR, but their aggregation behaviors and influence on polyisoprene properties during storage and use have not yet been revealed at the molecular level. To begin to address these phenomena, two sequentially different polyisoprene copolymers were suspended with phosphorylcholine groups to disclose their influence on phase separation, network dynamics, mechanical properties, and crystallization differences. Phosphorylcholine groups attached to polymer chains can form aggregates that increase the storage modulus of rubbers, and this process is accelerated at elevated temperatures due to faster chain movement. In addition, phosphorylcholine groups act as crosslinking points in unvulcanized and vulcanized rubbers and increase mechanical properties by promoting strain-induced crystallization (SIC). By contrast, the polymers with pendant hydroxyl groups present sequence-dependent SIC properties that are ascribed to their non-aggregation nature.