Conventional CFD-based shape optimization technology that uses parametric shape modification and optimal solutions searching algorithms has the two problems: (1) outcome of optimized shapes depend on the selection of design parameters made by the designer, and (2) high computational costs. To resolve those problems, two innovative inverse analysis technologies based on the Adjoint Method were developed in previous study: surface geometry deformation sensitivity analysis to identify the locations to be modified, and topology optimization to generate an optimal shape for maximizing the cost function in the constrained design space. However, these technologies are only applicable to steady flows. Since most flows in a vehicle (such as engine in-cylinder flow) are transient, a practical technology for surface geometry sensitivity analysis has been developed based on the Transient Adjoint Method. This can be applied to fully transient flows like engine in-cylinder flow to calculate sensitivity distributions for arbitrary temporal performance in a targeted period utilizing transient flow results from commercially available CFD solvers. This was accomplished by introducing original discretized governing equations that are consistent with the Transient Adjoint theory and realistic flows including moving meshes and other events, as well as by developing methodologies for performing analysis stably and efficiently. This study confirmed that tumble flow rotation early in the compression stroke can be intensified taking into account pressure loss in the intake stroke of a stock engine by modifying the design shape of the intake port or piston according to the surface geometry sensitivity distribution calculated by the developed technology.