Pinning synchronization of a networked multi-agent system with a directed communication topology is investigated from a spectral analysis approach. Some new types of synchronized regions for networked systems with different nonlinear agent dynamics and inner coupling structures are discovered. The eigenvalue distributions of the coupling and control matrices for different types of directed networks are obtained. The effects of the network topology, pinning density and pinning strength on the network synchronizability are examined through extensive numerical simulations. It is shown that the synchronizability of the pinned network can be effectively improved by increasing pinning density and pinning strength for some types of synchronized regions, whereas too large the pinning density and pinning strength will lead to desynchronization for other types. It is found that directed random networks are not always easier to synchronize than directed small-world networks, and a denser eigenvalue distribution may not always imply better synchronizability.