Multiple kernel clustering (MKC) algorithms optimally combine a group of pre-specified base kernels to improve clustering performance. However, existing MKC algorithms cannot efficiently address the situation where some rows and columns of base kernels are absent. This paper proposes a simple while effective algorithm to address this issue. Different from existing approaches where incomplete kernels are firstly imputed and a standard MKC algorithm is applied to the imputed kernels, our algorithm integrates imputation and clustering into a unified learning procedure. Specifically, we perform multiple kernel clustering directly with the presence of incomplete kernels, which are treated as auxiliary variables to be jointly optimized. Our algorithm does not require that there be at least one complete base kernel over all the samples. Also, it adaptively imputes incomplete kernels and combines them to best serve clustering. A three-step iterative algorithm with proved convergence is designed to solve the resultant optimization problem. Extensive experiments are conducted on four benchmark data sets to compare the proposed algorithm with existing imputation-based methods. Our algorithm consistently achieves superior performance and the improvement becomes more significant with increasing missing ratio, verifying the effectiveness and advantages of the proposed joint imputation and clustering.