Phenolation is one of the most efficient ways to improve lignin's reactivity by increasing phenolic hydroxyl (Ph-OH) contents and active sites. However, due to its complex structural nature, the lignin structure significantly impacts the phenolation and its following nanoparticle fabrication. In this study, phenolation of cellulolytic enzyme lignin (CEL) and kraft lignin (KL) of Simao pine was conducted under appropriate acidcatalyzed conditions and the resultant phenolated lignins were comprehensively characterized. The main structural difference between KL and CEL arises from the content of β-aryl ether bonds, leading to varied increments of Ph-OH contents in phenolation. Size-controlled lignin nanoparticles (LNPs) were successfully prepared from phenolated lignins with lower molecular weight, lower aliphatic-OH content, and higher level of Ph-OH groups. The average diameters and surface charges of LNPs varied from 60 to 120 nm and −30 to −55 mV, respectively, which highly depended on the phenolation degree of lignin, especially the content of Ph-OH groups. It indicates that the structural features of phenolated lignin could facilitate LNP fabrication with tunable sizes. This study reveals the structural influences on lignin phenolation and its nanoparticle fabrication, providing new insights into the size-controlled design, preparation, and application of LNPs.