Population cycles that persist in time and are synchronized over space pervade ecological systems, but their underlying causes remain a long-standing enigma. Here we examine the synchronization of complex population oscillations in networks of model communities and in natural systems, where phenomena such as unusual ‘4- and 10-year cycle’ of wildlife are often found. In the proposed spatial model, each local patch sustains a three-level trophic system composed of interacting predators, consumers and vegetation. Populations oscillate regularly and periodically in phase, but with irregular and chaotic peaks together in abundance—twin realistic features that are not found in standard ecological models. In a spatial lattice of patches, only small amounts of local migration are required to induce broad-scale ‘phase synchronization’, with all populations in the lattice phase-locking to the same collective rhythm. Peak population abundances, however, remain chaotic and largely uncorrelated. Although synchronization is often perceived as being detrimental to spatially structured populations, phase synchronization leads to the emergence of complex chaotic travelling-wave structures which may be crucial for species persistence.