Interacting with digital contents in 3D is an essential task in various applications such as modeling packages, gaming, virtual reality, etc. Traditional interfaces using keyboard and mouse or trackball usually require a non-trivial amount of working space as well as a learning process. We present the design of EZ-Manipulator, a new 3D manipulation interface using smartphones that supports mobile, fast, and ambiguity-free interaction with 3D objects. Our system leverages the built-in multi-touch input and gyroscope sensor of smartphones to achieve 9 degrees-of-freedom axis-constrained manipulation and free-form rotation. Using EZ-Manipulator to manipulate objects in 3D is easy. The user merely has to perform intuitive single- or two-finger gestures and rotate the hand-held device to perform manipulations at fine-grained and coarse levels respectively. We further investigate the ambiguity in manipulation introduced by indirect manipulations using a multi-touch interface, and propose a dynamic virtual camera adjustment to effectively resolve the ambiguity. A preliminary study shows that our system has significant lower task completion time compared to conventional use of a keyboard–mouse interface, and provides a positive user experience to both novices and experts.