Auxetic structures made of biodegradable polymers are favorable for industrial and daily life applications. In this work, poly(butylene adipate-co-terephthalate) (PBAT) is chosen for the study of the deformation behavior of an inverse-honeycomb auxetic structure manufactured using the fused filament fabrication. The study focus is on auxetic behavior. One characteristic of polymer deformation prediction using finite element (FE) simulation is that no sounded FE model exists, due to the significantly different behavior of polymers under loading. The deformation behavior prediction of auxetic structures made of polymers poses more challenges, due to the coupled influences of material and topology on the overall behavior. Our work presents a general process to simulate auxetic structural deformation behavior for various polymers, such as PBAT, PLA (polylactic acid), and their blends. The current report emphasizes the first one. Limited by the state of the art, there is no unified regulation for calculating the Poisson’s ratio ν for auxetic structures. Here, three calculation ways of ν are presented based on measured data, one of which is found to be suitable to present the auxetic structural behavior. Still, the influence of the auxetic structural topology on the calculated Poisson’s ratio value is also discussed, and a suggestion is presented. The numerically predicted force–displacement curve, Poisson’s ratio evolution, and the deformed auxetic structural status match the testing results very well. Furthermore, FE simulation results can easily illustrate the stress distribution both statistically and local-topology particularized, which is very helpful in analyzing in-depth the auxetic behavior.