The exacerbation of inherent light scattering with increasing scintillator thickness poses a major challenge for balancing the thickness-dependent spatial resolution and scintillation brightness in X-ray imaging scintillators. Herein, we fabricated a thick pixelated needle-like array scintillator capable of micrometer resolution via waveguide structure engineering. Specifically, this involves integrating a straightforward low-temperature melting process of manganese halide with an aluminum-clad capillary template. In this waveguide structure, the oriented scintillation photons propagated along the well-aligned scintillator and were confined within individual pixels by the aluminum reflective cladding, as substantiated from the comprehensive analysis including laser diffraction experiments. Consequently, thanks to isolated light-crosstalk channels and robust light output due to increased thickness, ultra-high spatial resolutions of 60.8 lp mm−1 and 51.7 lp mm−1 at an MTF of 0.2 were achieved on 0.5 mm and even 1 mm thick scintillators, respectively, which both exceed the pore diameter of the capillary arrays template (Φ = 10 μm). To the best of our knowledge, these micrometer resolutions are among the highest reported for metal halide scintillators and have never been demonstrated on such thick scintillators. This work presents an avenue to the demand for thick scintillators in high-resolution X-ray imaging across diverse scientific and practical fields.