Intake pipe structure has a pivotal impact on the distribution of vortices within the combustion chamber in a cycloidal rotary engine (CRE). Therefore, studying the influence of the intake pipe deflection angle (IPDA) on the in-cylinder airflow motion has significant importance for enhancing CRE performance. This study utilized computational fluid dynamics and chemical reaction kinetics methods to establish a numerical simulation model for the in-cylinder flow and combustion in the CRE. Subsequently, the Omega vortex identification method was employed to investigate the influence of IPDA on the vortex structures within the cylinder and to explore the relationship between CRE performance and the vortices. The research findings indicate that although the IPDA did not significantly alter the fuel mass injected into the cylinder, it increased the airflow velocity by 14.6% during the main intake stage and increased the mass fraction of the burned fuel at the compression top dead center by 19.1%. Additionally, the increased airflow velocity within the cylinder led to improvements in both the mean tumble ratio by 186.5% and the turbulent kinetic energy by 25.5%. Furthermore, the IPDA significantly changed the distribution of vortices within the cylinder, which is a key factor contributing to the combustion variation of the CRE. The case of IPDA = 16° provided the largest volume of the strong vortices and the highest mean in-cylinder pressure. Compared to the original design, the volume of strong vortices was 1323.6% greater, and the mean in-cylinder pressure was higher by 5.3%.