In this paper, we investigate the impacts of transmitter and receiver windows on orthogonal time-frequency space (OTFS) modulation and propose a window design to improve the OTFS channel estimation performance. Assuming ideal pulse shaping filters at the transceiver, we first identify the role of window in effective channel and the reduced channel sparsity with conventional rectangular window. Then, we characterize the impacts of windowing on the effective channel estimation performance for OTFS modulation. Based on the revealed insights, we propose to apply a Dolph-Chebyshev (DC) window at either the transmitter or the receiver to effectively enhance the sparsity of the effective channel. As such, the channel spread due to the fractional Doppler is significantly reduced, which leads to a lower error floor in channel estimation compared with that of the rectangular window. Simulation results verify the accuracy of the obtained analytical results and confirm the superiority of the proposed window designs in improving the channel estimation performance over the conventional rectangular or Sine windows.