A clear elucidation of structural feature of whole lignin in plant cell wall is of great importance for understanding lignin biosynthesis mechanism and developing lignin based chemicals or materials under the current biorefinery scenario. Swollen residual enzyme lignin (SREL) has been identified as an ideal representative for native lignin in the plant walls. To investigate the influence of preswelling conditions on the structural features, the SREL obtained through preswelling the ball-milled Eucalyptus wood powder in 2, 4 and 8% NaOH solutions and subsequent in-situ enzymatic hydrolysis were thoroughly characterized. A cellulolytic enzyme lignin (CEL) was also prepared as a comparison. The quantitative NMR analyses indicated that the relative contents of β-O-4' linkages in SRELs were higher than that in CEL. The lignin structure tended to undergo more destruction with the elevated NaOH concentration. A relatively low NaOH concentration (2% in this study), which could be applied to effectively remove hemicelluloses and transform cellulose structure from cellulose I to cellulose II, was competent to prepare SREL as an ideal representative for the protolignin. An optimization of SREL preparation was essential for a better understanding of the whole protolignin.