Under the megacompetition in globalizing economy while facing long lasting economic stagnation, the effective utilization of potential resources for innovation has become a crucial strategy for R&D intensive industries. The construction of a smart cooperative R&D structure has thus become significant. Among Japan's R&D intensive industries, the transport machinery industry has constructed an effective cooperative R&D structure by smartly complementing both comparatively advantageous and disadvantageous technologies by means of integrating the effective utilization of technology spillover and joint collaborative R&D.Prompted by this complementing system, this paper attempts to elucidate the mechanism enabling the transport machinery industry to construct the smart cooperative R&D structure. Resonant R&D structure is identified as a source of such R&D cooperation leading to increasing its marginal productivity of technology.