The rapid evolution of the Unmanned Aerial Vehicle (UAV) industry has significantly increased interest in UAV design with trans-domain capabilities. It is still a major challenge to achieve miniaturization and enhance the maneuverability and underwater reliability of trans-domain UAVs. In this paper, a novel bullet shape Trans-Domain Amphibious Vehicle (TDAV) is proposed which achieves free trans-domain motion and has the advantages of small size, high maneuverability and high reliability for both rotary-wing UAV and Autonomous Underwater Vehicle (AUV) operation. Compared with traditional amphibious machines, the TDAV design is streamlined and thus inherits the advantages of both the Bamboo Dragonfly and underwater AUVs. The proposed TDAV has a coaxial counter-propeller-tilting platform which satisfies the power and small diameter fuselage requirements, and the blades fold to reduce underwater drag and facilitate transportation. Further, a stable and efficient trans-domain attitude adjustment system is presented which effectively realizes trans-domain attitude switching. Based on the characteristics of the symmetric TDAV body, a rudder blade allocation algorithm is proposed to realize free movement in water. Finally, an improved particle swarm optimization algorithm is used to obtain suitable hierarchical fractional-order PID parameters. Both simulation and outdoor tests were performed and the results demonstrate that the proposed TDAV achieves outstanding performance in terms of lift altitude, trans-domain attitude switching time, and free trans-domain movement in both water and air.