For formulating Quadratic Knapsack Problems (QKPs) into the form of Quadratic Unconstrained Binary Optimization (QUBO), it is necessary to introduce an integer variable, which converts and incorporates the knapsack capacity constraint into the overall energy function. In QUBO, this integer variable is encoded with auxiliary binary variables, and the encoding method used for it affects the behavior of Simulated Annealing (SA) significantly. For improving the efficiency of SA for QKP instances, this paper first visualized and analyzed their annealing processes encoded by conventional binary and unary encoding methods. Based on this analysis, we proposed a novel hybrid encoding (HE), getting the best of both worlds. The proposed HE obtained feasible solutions in the evaluation, outperforming the others in small- and medium-scale models.