As the main content of postgraduate education, innovation capacity cultivation is closely related to graduate quality. Today, many problems, including poor sense of innovation, lack of innovative thinking, and weak practical ability become prominent, along with the dramatic increase in the number of graduate students. As a result, graduate groups can hardly adapt themselves to violent social competitions and tough employment environment. This paper analyzed the problems existing in innovation capacity cultivation of postgraduates majored in civil engineering, with consideration of conditions and characters of agriculture and forestry universities. It is suggested that reforming of curricula setup, paying more attention to foreign language teaching, cultivating practical ability and conducting innovation research in interdisciplinary fields should be emphasized for postgraduates' innovation capacity improving, civil engineering discipline developing, and healthy graduate employments.