In this article, preliminary and conceptual design, dynamic modeling and flight dynamics modes of an unmanned aerial vehicle which have both helicopter flight mode and fixed-wing aircraft flight mode is researched. The air vehicle (ZANKA-IV) which will be produced in Erciyes University Faculty of Aeronautics and Astronautics Drone Laboratory captures both passive and active morphing properties. Furthermore, this hybrid unmanned aerial vehicle (HUAV) will be controlled by PID based autopilot system. In this paper, as the first time, sizes of morphing apparatuses and autonomous system are determined simultaneously in order to maximize autonomous flight performance. A stochastic optimization method is applied for simultaneous design. As a result, optimum solution is obtained very fast and accurately. Moreover, as a result of this approach, autonomous control of HUAV becomes noticeably efficient.  10% improvement in autonomous performance index is achieved. Furthermore, the autopilot successfully tracks a reference trajectory with pitching angle of 30 degrees.