The heat transfer area of the heater tubes is a significant factor that deeply affects net output power and thermal efficiency in Stirling engines. It is greatly affected by the input heat transfer rate, heater tube geometries, and heat transfer removal rate. The alpha Stirling engine heater is our concern in this study. An ordinary circular and straight elliptical section heater tubes having different twisting ratios with a rectangular section-connecting duct are used to study the different heater tube configurations and twisting effect on the heat transfer characteristics and working fluid motion inside the engine. Three twisting ratios of two, three, and four with each section of the heater tube are used in this study. The 3D simulation model using the SST K-ω model using ANSYS FLUENT-16 is used for simulating airflow through the hot cylinder, heater tubes, regenerator, cooler, and cold cylinder of the Stirling engine, during a complete engine cycle. The results showed that increasing the twisting value increases the net output power and the thermal efficiency. The maximum net power output occurs at the elliptical section heater tube with a two-twist ratio with a value of 1249.26 W by an increase of 86.90 W with respect to the ordinary circular heater. In addition, the maximum thermal efficiency occurs at the elliptical section heater tube with a two-twist ratio with a value of 29.55% by an increase of 1.07% with respect to the ordinary circular heater.