As dominant ecosystems on protected tropical and subtropical shorelines, mangroves are globally important for essential ecosystem services such as acting as nursery habitat for juvenile nekton, land building and coastal protection. The structural complexity associated with the aerial roots of mangroves strongly underpins these services. However, due to the lack of a satisfactory method for measuring and quantifying this complexity, the relationship between complexity and mangrove ecosystem services is still obscure. The objectives of this study were (1) to find a low-cost method for realistically quantifying habitat complexity; and (2) to assess the importance of habitat structural complexity to the principal ecosystem services offered by mangroves, namely, supporting fish assemblage, flow attenuation and sediment trapping. An innovative, simple, and low-cost method based on an RGB_D scanning sensor (Kinect) and free and readily accessible software (Meshlab, Matlab, Qubicle Constructor and Voxeliser) was used to capture realistic 3D models of mangrove aerial roots. This low-cost approach provides a novel method to capture and measure structural complexity at a mesoscale in a full 3D approach, enabling an analysis of the relationship between habitat complexity and mangrove ecosystem services. The fractal dimension (FD) and AVR (area/volume ratio of the 3D model) indices were developed to quantify mangrove root structural complexity. The cube counting method was used for three-dimensional characterisation of FD of the space around aerial roots. To assess the apparent complexity of the structure to fish potentially using the roots, rectangular prisms with dimensions corresponding to the allometry of the fish were used to estimate the FD values.