Evaluating cognitive ability and skills development in higher education presents challenges because the focal outcome often serves as, or at least is reflected in, selection criteria for college admission decisions. Additionally, the baseline abilities and skills gained from earlier educational experiences impact students' further learning outcomes. To address these challenges, we propose an integrated framework for estimating students' growth that accounts for lasting transition effects and varying selection effects. Using a nationally representative longitudinal sample of Chinese university students, we found that students experienced medium-sized growth (0.67) in critical thinking skills, with a large effect size observed for evaluating the reasoning of an argument, a medium effect size for evaluating argument implications, and no significant growth in evaluating argument credibility. Our estimates of transition effects showed that the impact of earlier education experience on students' critical thinking growth diminished in the college years. After controlling students' socioeconomic status and the college entrance examination scores, we found that the within-university advantage in the college entrance examination served as a factor in explaining the university impacts on students’ critical thinking. Our findings provide rich insights into improving the evaluation of critical thinking skills in Chinese universities, and our illustrative framework can also be applied to similar education contexts.