The material removal rate (MRR) is an important variable but difficult to measure in the chemical–mechanical planarization (CMP) process. Most data-based virtual metrology (VM) methods ignore the large number of unlabeled samples, resulting in a waste of information. In this paper, the semi-supervised deep kernel active learning (SSDKAL) model is proposed. Clustering-based phase partition and phase-matching algorithms are used for the initial feature extraction, and a deep network is used to replace the kernel of Gaussian process regression so as to extract hidden deep features. Semi-supervised regression and active learning sample selection strategies are applied to make full use of information on the unlabeled samples. The experimental results of the CMP process dataset validate the effectiveness of the proposed method. Compared with supervised regression and co-training-based semi-supervised regression algorithms, the proposed model has a lower mean square error with different labeled sample proportions. Compared with other frameworks proposed in the literature, such as physics-based VM models, Gaussian-process-based regression models, and stacking models, the proposed method achieves better prediction results without using all the labeled samples.