For the characterization of heterogeneous aquifers, transient hydraulic tomography (THT) was proposed as a promising method to obtain the distribution of hydraulic parameters with satisfying spatial resolution using different approaches. These include hydraulic travel time, attenuation inversions, thermal tracer tomography, and geostatistical inversion with successive linear estimator (SLE). For the same hydrogeological test, different inversion methods tend to use different sub-data sets to obtain different hydraulic parameters. Up to now, however, few studies have focused on revealing the respective characteristics of these inversion methods and attempted to improve the accuracy of aquifer characterization by bridging the shortcomings of the inversion methods. The main objective of this study was to evaluate the utility of multiple inversion techniques on aquifer heterogeneity characterization. A series of warm water injection tests were first simulated in a fluvial aquifer analogue outcrop. The calculated head and temperature datasets from these tests were fully utilized to reveal the aquifer heterogeneity by using all of the four above-mentioned inversion methods. The results show that the thermal tracer tomography, hydraulic travel time, and attenuation tomography characterized the high permeability zones more accurately within the well area, whereas the geological statistical method tended to depict the overall distribution of K values for a larger area. By comparison analysis and combinations of the individual inversion results, the scientific and economic complementarity can be studied and some valuable advice for the choice of different inversion methods can be recommended for future practices.