Radar altimetry is useful for monitoring water surface dynamics in an era of satellite remote sensing. One of the uses of satellite altimetry is to evaluate/calibrate the hydrodynamic model or to improve river-related variables by optimization/assimilation methods. However, with the discrete nature of the hydrodynamic models, comparing simulated water surface elevation (WSE) with satellite altimetry is challenging due to the difficulty in the exact matching of representative locations by satellite altimetry virtual station (VS) and model grids. We developed an algorithm to assign the VSs to the river network and labeled each VS with a flag according to the characteristics of the allocation to the river network. We presented an altimetry mapping procedure (AltiMaP) to allocate VS locations given in the HydroWeb database (https://hydroweb.theia-land.fr/) to the MERIT Hydro (http://hydro.iis.u-tokyo.ac.jp/~yamadai/MERIT_Hydro/) river network. Each VS was assigned to the nearest river in the MERIT Hydro considering the geometric distance. During the altimetry mapping, flags were added to each VS depending on the method of allocation. The flags were added in cases if the latitude-longitude of VSs is identified as a single-channel river (Flag 10); as a land pixel and allocated to the nearest single-channel river (Flag 20); as a multi-channel river (Flag 30); and as an ocean pixel and allocated to the nearest river (Flag 40). We allocated more than 12000 VSs in which most of the VSs were allocated as Flag 10 which accounts for 71.7% of all VSs. Moreover, most of the Flags 10 and 20 are located up and mid-streams whereas Flags 30 and 40 were in downstream river reaches. The biased VSs which have a large elevation difference between the mean observed WSE with the model elevation were approximately 0.8% of the total VSs and were mostly seen in narrow rivers at high elevations. The error of simulated WSE by a global river hydrodynamic model was reduced by 10.6% by employing the AltiMaP against the allocation VSs by converting longitude and latitude information to the coarse resolution river network. Therefore, the allocation of VSs using the method developed in this study (AltiMaP) to the river network enhanced the comparability of the simulated WSE by the global hydrodynamic model against satellite altimetry. The AltiMaP algorithm and data will be useful for the global hydrological community.