The recent advancements in Photon-counting computed tomography have revolutionized spectral imaging, providing unparalleled high-resolution visualization and enhanced material discrimination. This study presents and evaluates a state-of-the-art in-house developed photon-counting micro-CT system (micro-PCCT) capable of reaching voxel resolutions below 20 micrometers. The system's sophisticated design facilitates complete, non-invasive internal analyses through comprehensive rotational scans, thereby enabling the precise delineation of internal structures and the construction of detailed three-dimensional representations that offer deeper insights into material and functional properties of samples. Comprehensive evaluation points to the micro-PCCT system's exceptional capacity to accurately quantify photon counts over a wide energy spectrum, thus facilitating the assembly of detailed energy signatures. Its ability to generate acutely transparent and intricately detailed CT imagery across a spectrum of energy levels marks a considerable enhancement over traditional technologies. The analytical findings, underscored by a line graph illustrating variations in sample density and composition, confirm the performance of developed micro-PCCT system. Our investigation underscores the pre-clinical advantages of our micro-PCCT over traditional imaging techniques, highlighting improved contrast-to-noise ratios, reduced image noise, advanced material identification and enhanced spatial resolution, all achieved at lower radiation doses. A micro-PCCT simulation platform, developed using the Geant4 Monte Carlo toolkit and thoroughly validated against actual measurements, demonstrates significant promise for the application of micro-PCCT in spectral imaging. This study not only affirms the system's leading-edge performance but also paves the way for future developments and expanded use in spectral imaging applications.