Against the backdrop of the digital economy and the construction of emerging engineering disciplines, this paper proposes and constructs a training model for excellent scientific and technological innovation talents, bridging undergraduate and graduate studies in software engineering, characterized by “integrated objectives, project-driven learning, and the integration of science and education.” This model aims to cultivate outstanding scientific and technological innovation talents as its overall goal, achieving seamless integration of undergraduate and graduate ability cultivation through the construction of a hierarchical and progressive objective system. It establishes a comprehensive five-level progressive project training system to bridge the gap between undergraduate practice and graduate research, and sets up a deeply integrated mechanism for the collaboration of science, education, and industry to promote the transformation of scientific research and industrial resources into teaching. Additionally, it improves the support system from three aspects: institutional frameworks, evaluation, and incentives. The study also outlines a five-stage practical path: “top-level design–resource integration–pilot operation–comprehensive promotion–dynamic optimization.” This model effectively breaks down the barriers between undergraduate and graduate training, strengthens students’ scientific research innovation and engineering practice abilities, and provides a replicable practical paradigm for the training of scientific and technological innovation talents bridging undergraduate and graduate studies in engineering disciplines.