Abstract : A main challenge in the development of new detectors is the achievement of a satisfactory comprehension of the instrument behaviour. We present the simulation work developed to understand and characterize an innovative micro-CT scanner. The PIXSCAN scanner is a photon counting device based on hybrid pixel detectors. Its working principle is expected to improve the contrast for soft tissues and to reduce both the scan duration and the dose absorbed by the animal. A prototype of the scanner, PIXSCAN-XPAD2, has been assembled and studied in order to achieve a proof of principle of the system. The image quality of the demonstrator is affected by a number of limiting factors. The estimation of the intrinsic properties of the imaging system can be achieved by an unfolding of the different degrading elements. For this, both an analytical and a Monte Carlo simulation of the prototype and of the evaluation phantoms have been developed to ensure a satisfactory comprehension of the data. The Monte Carlo simulation was based on the GATE package. It included the complete simulation of photon propagation in matter, together with the modelling of the source spectrum, the scanner geometry and the sensor response. The analytical simulation was much more approximate, its merit was the rapidity which permitted fast preliminary results. Several figures of merit were studied and showed good agreement with real data (see figure 1 and figure 2 as example). Hence, the developed simulations can be used as a valid tool for the estimation of the ultimate PIXSCAN performances, in terms of spatial resolution, contrast measurement and dose reduction.