Terahertz (THz) wave induced biological impact is concentrating focus. THz wave is being a promising external bioelectric signal adjusting method, especially calcium signals. In this work, molecular dynamics simulation is carried out on TRPV6, a calcium-selective channel, to preliminarily assess the effect of THz waves on its structure and Ca2+ permeation function. TRPV6 is a typical tetrameric ion channel; its ion pore owes a selectivity filter, central cavity, gate, and a special helix bundle crossing region. The infrared spectrum, ion pore radius pro-file, and the potential of mean force of Ca2+ permeation has been calculated to assess the effects of THz waves on TRPV6. The vibrational spectrum shows 3 typical peaks about the carboxyl and carbonyl groups. Moderate THz waves in specific frequencies (42.85 and 51.07 THz) can trigger structural changes in specific regions but not greatly affect the whole channel structure. The PMF of Ca2+ transport shows that the backbone fluctuation of TRPV6 plays a negative role in its Ca2+ permeation function and attraction of the central cavity.