The objectives of this study were to visualise and quantify the soil macropore networks and root architectures within intact soil columns under different ecosystems and to investigate the influences of roots on soil macropore network characteristics. Intact soil columns with diameters of 110 mm and lengths of 400 mm were taken from alpine Kobresia meadow, interspace meadow patches of Potentilla fruticosa shrubs, Potentilla fruticosa shrubs and Artemisia sphaerocephala shrubs in the Qinghai Lake watershed of the NE Qinghai-Tibet Plateau. A Philips medical X-ray CT scanner was used to simultaneously visualise and quantify the soil macropore networks and root architectures. The results showed that macropores and taproots were concentrated in the top 0-150 mm. The root volume density of the P. fruticosa shrub was greater than that of the interspace meadow patches of P. fruticosa shrub and that of the alpine Kobresia meadow. The macroporosity and the root volume density of the soils under the P. fruticosa shrub patches were significantly greater than those in the soils under the other sites. The root volume density was significantly correlated with the macroporosity for the A. sphaerocephala shrubs (R 2 = 0.88) and the P. fruticosa shrubs (R 2 = 0.73). There were significant positive correlations between the volume density, branch density and mean angle of the roots and those of the macropores. Shrub roots invasion played an important role in the formation of macropores. The root volume density was the most important factor for the quantified characteristics and distributions of the macropores.