When printing Polyamide 6 (PA6) material using Fused Deposition Modeling (FDM) technology, warping and delamination of the printed structure are common issues that severely affect product quality. To analyze the causes of warping and delamination during the FDM process of PA6, a subroutine for a dual-ellipsoid heat source model, Dflux, was developed. Finite element simulation was used to model the FDM process of PA6, combined with a single-factor experimental scheme, to investigate the effects of nozzle temperature and printing speed on the temperature field during the melting and forming process of a double-layer structure. The study aimed to explore the mechanisms of warping and delamination in PA6. The results indicated that when molten PA6 is extruded and deposited, the material begins to cool and contract, leading to uneven shrinkage of the printed layers. This uneven shrinkage causes structural deformation. Among the factors studied, the nozzle temperature has a more significant impact on warping and delamination than the printing speed. Lower nozzle temperatures and higher printing speeds tend to reduce the likelihood of delamination. However, excessively low nozzle temperatures can lead to warping deformation of the structure.