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In this paper, we proposed a distributed hierarchical flow balancing (HFB) protocol for data aggregation in wireless sensor networks. A clustering algorithm is firstly proposed to group several sensors into one cluster based on the overlapping degrees of those sensors. Then, a backbone construction algorithm is proposed to construct a multi-level backbone network using the cluster heads. Furthermore, a flow balancing algorithm is designed to convey the sensed data from sensors to the sink. Lastly, a rerouting algorithm is proposed to reconstruct the network topology only around the locations where some cluster heads run out of their energy and drop out from the backbone. The proposed scheme has been evaluated in comparison with previous approaches using simulations. The simulation results show that HFB yields much longer lifetime than the others.