In this paper we study partially linear varying coefficient models with missing covariates. Based on inverse probability-weighting and B-spline approximations, we propose a weighted B-spline composite quantile regression method to estimate the non-parametric function and the regression coefficients. Under some mild conditions, we establish the asymptotic normality and Horvitz–Thompson property of the proposed estimators. We further investigate a variable selection procedure by combining the proposed estimation method with adaptive LASSO. The oracle property of the proposed variable selection method is studied. Under a missing covariate scenario, two simulations with various non-normal error distributions and a real data application are conducted to assess and showcase the finite sample performance of the proposed estimation and variable selection methods.