The pristine and acetylated cellulose nanocrystal (CNC) particles were incorporated with poly(epsilon-caprolactone) to prepare two kinds of green nanocomposite systems: the former is incompatible, while the latter compatible thermodynamically. A rheological study was then performed systematically with various flow fields, including linear and nonlinear dynamic shear flow, creep and start-up flow. Some interesting results were shown then. The pristine CNC filled system shows far lower percolation threshold than the acetylated CNC filled one because the improved phase affinity yields diluent effect. The formation and rebuild-up of percolated network is driven by the Brownian motion of particles, which are nearly independent of altered phase affinity. However, the improved phase affinity makes the system more sensitive to the strain-responded deformation, leading to the reinforced Maxwell spring unit during creep and to a weak strain overshoot during dynamic flow. The structural evolution and relaxations of two systems were further evaluated from different perspectives. (C) 2018 Elsevier Ltd. All rights reserved.