This paper aims to investigate the crushing behaviour and protective performance of an innovative auxetic structure, named the hourglass structure (HGS), under in-plane compressive loads. The HGS was fabricated with a 3D printing method through fused filament fabrication technique. The 3D printed HGS specimens were subjected to a displacement-controlled in-plane quasi-static compressive load. A 3D comprehensive numerical model was developed and calibrated with the experimental results. The calibrated numerical model was used for a parametric study to explore the effects of relative density, functional grading, and crushing velocity on the protective performance of the HGS. Furthermore, a theoretical model was proposed to correlate plateau stress of the HGS with geometric design parameters, effective Poisson’s ratio, and matrix material properties. Verified with a series of numerical analyses of different HGS designs, the proposed theoretical model predicted plateau stress with less than 10% relative error. In addition, experimental, numerical, and theoretical analyses uncovered load–deformation relationship, Poisson’s ratio, crushing mechanism, and energy absorption capacity of the novel auxetic. Overall, the HGS exhibited excellent features for protective engineering applications such as shock mitigation and blast energy absorption.