Satellite FH (frequency hopping) anti-jamming communication systems were studied. Based on analyses of effects of jamming on frames that belongs to the link layer, a measurement, link frame throughput was proposed. In addition, a cross-layer designed time-frequency diversity strategy was suggested to improve anti-jamming performance of the system on the measurement of link frame throughput. The strategy makes full use of "dodging" characteristic of FH signals to decrease the probability that the FH signals are hit by jamming. For comparison, another strategy, deep interleaving strategy processed on the physical layer was also analyzed. Results of numerical analyses and simulations show that the throughput performance of the time-frequency diversity strategy is better than that of the deep interleaving strategy. The advantages of the strategy are lower complexity and shorter delay. It could be used to provide further protection from jamming.