Spatial navigation is a crucial ability involving the interplay of multiple cognitive processes and is related to input spatial information (such as landmarks and orientation cues) and output navigational strategies (such as route-based and map-based). It is still not clear where is the spatial navigation system and whether these tasks evoke different activation patterns in human brain. Thus, we analyzed the reported brain activations of 33 related functional neuroimaging studies by using activation likelihood estimation (ALE) meta-analyses. Statistical analysis revealed a navigational system including the hippocampus, parahippocampal place area (PPA), retrosplenial complex (RSC), occipital place area (OPA), and insula. More likely, landmarks activate the left secondary motor cortex (SMC), whereas orientation cues activate the right somatosensory associative cortex (SAC). Although no region showed stronger activation likelihood in route- than map-based navigation, the map-based navigation had stronger activation likelihood in the right SAC than route-based navigation. These findings revealed the brain representation of spatial navigational system and suggested that different parts of this system are involved with the specific navigational tasks.