Abstract Spiking neural networks (SNNs) are considered to be biologically plausible and power-efficient on neuromorphic hardware. However, unlike the brain mechanisms, most existing SNN algorithms have fixed network topologies and connection relationships. This paper proposes a method to jointly learn network connections and link weights simultaneously. The connection structures are optimized by the spike-timing-dependent plasticity (STDP) rule with timing information, and the link weights are optimized by a supervised algorithm. The connection structures and the weights are learned alternately until a termination condition is satisfied. Experiments are carried out using four benchmark datasets. Our approach outperforms classical learning methods such as STDP, Tempotron, SpikeProp, and a state-of-the-art supervised algorithm. In addition, the learned structures effectively reduce the number of connections by about 24%, thus facilitate the computational efficiency of the network.