A handheld electronic device and an operating method thereof are provided, in which at least two sets of sound outputting modules and sound receiving modules are disposed in the handheld electronic device. The operating method detects an orientation of the handheld electronic device by a motion detecting module and enables different sets of the sound outputting modules and the sound receiving modules according to a variation of the orientation of the handheld electronic device, so as to change a direction of a call operation, and thus a user can successfully make a phone call, even if the handheld electronic device is held upside down. Furthermore, the operating method can control the sound outputting modules and the sound receiving modules individually or collectively according to actual demands to achieve a multifunctional product design.