Micro laser powder bed fusion (μLPBF) is an additive manufacturing process enabling the fabrication of thin-walled metallic shell lattices at the micrometre scale. With wall thicknesses reduced down to 100 µm, this process significantly enhances the structural design freedom, enabling the design of multi-functional, lightweight, stiff, and strong components. However, from a manufacturing perspective, as the wall thicknesses approach the printing resolution, this process is likely to introduce geometric defects, and informed quality assurance of the 3D-printed structures becomes critical. From a structural perspective, the mechanical properties of thin-walled structures are known to be highly sensitive to manufacturing defects. To quantify the process-induced geometric defects and to understand the influences of the geometric defects on the mechanical properties of thin shell lattices, we propose a micro X-ray computed tomography (XCT) based finite element (FE) modelling methodology, which is validated here for Primitive-type shell lattices fabricated by μLPBF in stainless steel. Four types of geometric defects, namely thickness variations, through-thickness defects (holes) on shell surfaces, surface waviness and roughness, are incorporated into the shell element-based FE models. The detailed evaluation of numerical and experimental compression test results shows that the defect-informed simulation approach provides significantly improved prediction accuracy compared to the ideal geometry model in terms of stiffness, peak stress, plateau stress and densification behaviour. The respective influences of each type of defect and their combinations on the mechanical properties of the shell lattices are studied, highlighting that surface roughness and thickness variations lead to prominent impact on the reduction of both linear and nonlinear mechanical properties.