-This paper proposes a novel control strategy of a PV tracking system considering the shadow influence. If distance of between PV arrays is not enough, shadow can be occurred to PV module. In PV system, if shadow is occurred to PV modules then PV modules operates reverses bias, and will eventually cause hot-spot and loss. To reduce loss by shadow influence, this paper proposes shadow compensation algorithm using distance between arrays and shadow length of array. The distance between arrays is calculated by using azimuth of solar, and length of array shadow is calculated using by altitude of solar. The shadow compensation algorithm proposed in this paper compares distance between arrays and length of array shadow. When the shadow length is longer than the distance between arrays, the algorithm adjusts altitude of array to avoid the shadow effects. The control algorithm proposed in this paper proves validity through compared with conventional algorithm and proposes experiment result.