Coefficient of thermal expansion (CTE) characteristic of organic materials for substrates in flip chip package application demanded by semiconductor package requirements is becoming lower than ever. In general, height restrictions are imposed on package-on-package (PoP) devices in mobile applications. One should hence establish a tight budget on the height variation in manufacturing of the devices. Given such background, a lowering of the CTE characteristic of package substrates is an attractive solution for reducing package deformation upon manufacturing, since it contributes to minimize CTE mismatch of the substrates with silicon chips. In large-die flip chip applications such as high-end processors, a lower CTE substrate can mitigate mechanical stress not only on low-k layers in back end of the line (BEOL) underneath the chip bumps, but also on underfill layers during thermal cycling. Therefore an introduction of lower CTE materials in organic substrates is becoming essential for future applications of electronic devices. In this paper, thermal deformation behaviors of organic substrates associated with lowering of the CTEs of their constituent materials are analyzed by finite element analysis (FEA). The analyses are done on a 3-2-3 build-up layer structure substrate in order to focus onto typical application specific integrated circuit (ASIC) products. A finite element model for a test substrate is constructed by a method in which the substrate is divided into sections according to its circuitry patterns so that the lateral inhomogeneity of mechanical property is taken into account. The finite element analyses using the model showed that the package warpage decreases with lowering of the effective CTE of the substrate, but the warpage of the substrate itself increases and its surface profile changes from a concave shape to a convex shape. The analysis result of substrate warpage variation with the build-up material's CTE showed that the selection of build-up materials with appropriate material properties can contribute to reduce the substrate warpage. The analysis also showed that the adverse impact to the substrate's CTE reduction by such material selection is limited.