The use of cushioned insoles has been recommended as a method to reduce the impact forces on feet associated with running. This study is used to determine the influence of insole structure and thickness on the permeability and conductivity properties of air and temperature. The insoles are constructed with warp-knitted polyester spacer fabrics with 3D construction and have good cushioning, permeability, and conductivity properties. The middle layer is made up of polyester monofilament yarn which decides the thickness of fabric, and the two outer surfaces of the fabric were made from polyester multifilament yarns which is a closed and open structure. The comfort properties of spacer fabric have been studied by measuring air permeability, water vapor permeability, and thermal properties with respect to fabric porosity. One-way analysis of variance is used to analyze the significant of fabric thickness and surface structures. The experimental result shows that the vertical gap of the two outer surface layers and the horizontal pore size of the face surface decide the permeability and conductivity properties of spacer fabrics. The fabric with higher porosity show high permeability of air and water vapor. Depending on the fabric thickness and structure, the 4-mm thickness of spacer fabric with locknit structure resulted in low air and water vapor permeability. It is found that the 3.1-mm thickness spacer fabric with hexagonal net structure proves to have good air and water vapor permeability and comparatively lower thermal conductivity. © 2014, © The Author(s) 2014.