A new methodology “Combinatorial Computational Chemistry” was proposed to realize theoretical high-throughput screening of materials. In this review, we introduced our recent successful applications of combinatorial computational chemistry to material design. Especially, we succeeded in the development of huge number of new simulation programs for combinatorial computational chemistry. For example, our SCF-tight-binding quantum chemical molecular dynamics program is very effective to realize high-throughput screening, since it realizes more than 5,000 times acceleration. Furthermore, we succeeded in the development of multi-physics quantum chemical molecular dynamics program based on our SCF-tight-binding theory, which can simulate multi-physics phenomena including chemical reaction, shear, impact, stress, flow, electric field and so on. This new program realizes various process design in addition to material design on the basis of the combinatorial computational chemistry. We emphasized here that our new simulation programs are very powerful tool to realize high-throughput screening for both material and process design, which cannot be accomplished by the traditional first-principles approach.