The kernel function of Cauchy type for type BC is defined as a solution of linear q-difference equations. In this paper, we show that this kernel function intertwines the commuting family of van Diejen’s q-difference operators. This result gives rise to a transformation formula for certain multiple basic hypergeometric series of type BC. We also construct a new infinite family of commuting q-difference operators for which the Koornwinder polynomials are joint eigenfunctions.