Human navigation is generally believed to rely on two types of strategy adoption, route-based and map-based strategies. Both types of navigation require making spatial decisions along the traversed way although formal computational and neural links between navigational strategies and mechanisms of value-based decision making have so far been underexplored in humans. Here we employed functional magnetic resonance imaging (fMRI) while subjects located different objects in a virtual environment. We then modelled their paths using reinforcement learning (RL) algorithms, which successfully explained decision behavior and its neural correlates. Our results show that subjects used a mixture of route and map-based navigation and their paths could be well explained by the model-free and model-based RL algorithms. Furthermore, the value signals of model-free choices during route-based navigation modulated the BOLD signals in the ventro-medial prefrontal cortex (vmPFC), whereas the BOLD signals in parahippocampal and hippocampal regions pertained to model-based value signals during map-based navigation. Our findings suggest that the brain might share computational mechanisms and neural substrates for navigation and value-based decisions such that model-free choice guides route-based navigation and model-based choice directs map-based navigation. These findings open new avenues for computational modelling of wayfinding by directing attention to value-based decision, differing from common direction and distances approaches.