The COVID-19 pandemic has caused ~ 2 million fatalities. Significant progress has been made in advancing our understanding of the disease process, one of the unanswered questions, however, is the anomaly in the case/mortality ratio with Mexico as a clear example. Herein, this anomaly is explored by spatial analysis and whether mortality varies locally according to local factors. To address this, hexagonal cartogram maps (hexbin) used to spatially map COVID-19 mortality and visualise association with patient-level data on demographics and pre-existing health conditions. This was further interrogated at local Mexico City level by choropleth mapping. Our data show that the use of hexagonal cartograms is a better approach for spatial mapping of COVID-19 data in Mexico as it addresses bias in area size and population. We report sex/age-related spatial relationship with mortality amongst the Mexican states and a trend between health conditions and mortality at the state level. Within Mexico City, there is a clear south, north divide with higher mortality in the northern municipalities. Deceased patients in these northern municipalities have the highest pre-existing health conditions. Taken together, this study provides an improved presentation of COVID-19 mapping in Mexico and demonstrates spatial divergence of the mortality in Mexico.