Using ATP as a fuel, conventional kinesins take unidirectional steps along the single protofilament of microtubule through the alternated binding of two motor domains to the binding sites. The structural changes of kinesin motors are closely coupled to the ATP binding and its subsequent hydrolysis. Although a number of experimental efforts have been made to elucidate the physical principle of kinesin dynamics, schematically summarized in a mechanochemical cycle, limitations in the spatial and temporal resolution of current experiments have prevented a straightforward understanding of kinesin dynamics based on its microscopic structure. By exploiting a structure-based model of kinesin motor, we address a few selected issues on the kinesin dynamics. Firstly, our equilibrium ensemble of kinesin structures, whose both heads are bound to the microtubule binding sites, show that the internal tension (f?10-15 pN) built along the neck-linker exclusively disturbs the ATP binding pocket of the leading head from its native-like environment. This result clarifies the origin of kinesin’s high processivity, supporting the rearward strain induced regulation mechanism between the two motor domains. Secondly, we address the controversial issue of substep formation during the stepping motion. By solving the potential of mean forces experienced by kinesin’s tethered head relative to the microtubule surface and performing Brownian dynamics simulations, we show that stepping dynamics of kinesin motors is a complex process that hinges on the interplay between the dynamics of neck-linker zippering, diffusion, and geometry of microtubule surface. A transient trapping of kinesin head to the tubulin binding site in the adjacent protofilament can produce a substep in the averaged time trace. We estimate ?p ? 20 μs as the lower limit of neck-linker zippering time to observe the substep. Lastly, we show that partial unfolding of kinesin structure facilitates the binding kinetics of kinesin to the microtubule binding site.