Context. Galactic cosmic rays are widely assumed to arise from diffusive shock acceleration, specifically at shocks in supernova remnants (SNRs). These shocks expand in a complex environment, particularly in the core-collapse scenario as these SNRs evolve inside the wind-blown bubbles created by their progenitor stars. The cosmic rays (CRs) at corecollapse SNRs may carry spectral signatures of that complexity. Aims. We study particle acceleration in the core-collapse SNR of a progenitor with initial mass 60M and realistic stellar evolution. The SNR shock interacts with discontinuities inside the wind-blown bubble and generates several transmitted and reflected shocks. We analyse their impact on particle spectra and the resulting emission from the remnant. Methods. To model the particle acceleration at the forward shock of SNR expanding inside a wind bubble, we have initially simulated the evolution of the pre-supernova circumstellar medium by solving the hydrodynamic equations for the entire lifetime of the progenitor star. As the large-scale magnetic field, we have considered parameterised circumstellar magnetic field with passive field transport. Then, the hydrodynamic equations for the evolution of SNR inside the pre-supernova circumstellar medium have been solved simultaneously with the transport equation for cosmic rays in test-particle approximation and with the induction equation for the magnetohydrodynamics (MHD) in 1-D spherical symmetry.Results. The evolution of core-collapse SNRs inside complex wind-blown bubbles modifies the spectra of both the particles and their emission, on account of several factors including density fluctuations, temperature variations, and the magnetic field configuration. We have found softer particle spectra with spectral indices close to 2.5 during shock propagation inside the shocked wind, and this softness persists at later evolutionary stages. Further, our calculated total production spectrum released into the interstellar medium demonstrates spectral consistency at high energy with the galactic CRs injection spectrum, required in propagation models. The magnetic field structure effectively influences the emission morphology of SNR as it governs the transportation of particles and the synchrotron emissivity. There rarely is a full correspondence of the intensity morphology in the radio, X-ray, and gamma-ray bands.