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I am using georeferencer in QGIS to align a rater with a boundary shapefile, but after georeferencing, the resulting raster shifts a bit but does not shift completely to the GCP as it is supported to be. As illustrated in the image below, the circled area is supposed to be stretched to align with the red line above it but now there is a gap there. This problem goes away when using ArcGIS, but there is another problem with exported raster from ArcGIS so I prefer to do it in QGIS.

Does anyone know how to fix it?

georeferenced raster in QGIS:

enter image description here

georeferenced raster in ArcGIS:

enter image description here

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In QGIS you have many algorithms (transformation types) to choose from to georefence raster based on GCP (ground control points). I believe it is good idea to read about them a bit to understand what are the plus and cons of each of those, and how they transform the raster to match your GCP:

  • Linear
  • Helmet
  • Polyniomial 1,2,3
  • Thin Plate Spline
  • Projective

If you do not want to bother reading about transformation types, and you want respect GCP as much as possible, just use Thin Plate Spline.

If you like to know a bit more, you can start with another questions here: Transformation types in geo-referencing of QGIS? and Differences between different georeferencing transformation algorithms in QGIS

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