With the rapid development of modern industrial technology and high performance technology products, ultra-precision machining technology becomes increasingly important. However, joint clearance of kinematic pairs, lack of feeding accuracy and overlarge contact stress still limit the further improvement of ultra-precision machining technology. In this study, a novel surface machining method utilizing structural elastic waves was proposed, and a machining tool using the piezoelectric actuating principle was presented for verifying the proposed method. Two vibration modes with a phase shift of π/2 in both space and time domains are exited simultaneously in the elliptical motion of points on the structural surface. By means of adjusting driving signal parameters, such as frequency, voltage amplitude and phase shift, different machining performances could be achieved. The configuration and working vibration modes of the proposed machining tool were firstly calculated by the finite element method, and then the optimal working frequency of the machining tool prototype was determined by vibration characteristic experiments. At last, machining characteristic experiments were conducted to validate the proposed machining method. Experimental results showed that the minimum working contact force between the machining tool and workpiece was 1 N, and the chipped depth of 1.93 μm was achieved at the same contact force after machining for 5 min. And at the conditions of the contact force of 6 N, two driving voltages of 400 Vpp with a phase shift of π/2, and machining time of 5 min, the prototype could achieve to machine the workpiece most efficiently and the roughness of the machined workpiece surface could be reached approximating 0.20 μm. In conclusion, this proposed machining method could achieve a good quality machined surface with low residual stress and little damage by applying low contact force. Furthermore, it also had the advantage of no joint clearance error due to no kinematic pair in the structure, which improves the machining precision.