In this paper, we conduct a cross-layer analysis of both the jamming capability of the cognitiveradio-based jammers and the anti-jamming capability of the cognitive radio networks (CRN). We use a Markov chain to model the CRN operations in spectrum sensing, channel access and channel switching under jamming. With various jamming models, the jamming probabilities and the throughputs of the CRN are obtained in closed-form expressions. Furthermore, the models and expressions are simplified to determine the minimum and the maximum CRN throughput expressions under jamming, and to optimize important anti-jamming parameters. The results are helpful for the optimal anti-jamming CRN design. The model and the analysis results are verified by simulations.