Various micro-structure surface texturing methods have been used to produce optical functional surface in the grinding, such as the textured grinding wheel, wheel path control and off-spindle-axis grinding. However, those grinding technologies are inherently challenged to employ in large-scale surface grinding due to the extremely high requirement for wheel cutting profile dressing. In this study, a novel phase shift modulation based on wheel oscillation motion was proposed to generate the micro-structure array in ultra-precision grinding. The phase shift effect involved in the surface micro-structure generation is investigated, in which the role of the second phase shift on superimposed mode and micro-waviness forms is discussed. A theoretical model based on the tool superimposed oscillation is established to study the micro-structure texture generation mechanism by considering the second phase shift. The influence of modulation frequency in the case of phase shift and out of phase shift on the surface texture generation both for the striation pattern and micro-structure is compared to clarify the transition between the continuous grooves and the discrete micro-structure array. The study indicates that the phase shift modulation represents a novel paradigm for fabricating micro-structure array with considerable capability and high efficiency in ultra-precision grinding.