We study the problem of pricing variable annuities with a multi-layer expense strategy, under which the insurer charges fees from the policyholder's account only when the account value lies in some pre-specified disjoint intervals, where on each pre-specified interval, the fee rate is fixed and can be different from that on other interval. We model the asset that is the underlying fund of the variable annuity by a hyper-exponential jump diffusion process. Theoretically, for a jump diffusion process with hyper-exponential jumps and three-valued drift, we obtain expressions for the Laplace transforms of its distribution and its occupation times, i.e., the time that it spends below or above a pre-specified level. With these results, we derive closed-form formulas to determine the fair fee rate. Moreover, the total fees that will be collected by the insurer and the total time of deducting fees are also computed. In addition, some numerical examples are presented to illustrate our results.