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Is it possible to set tolerance value of geoprocessing tool on QGIS.

History is below. There are two polygon which have to be the same position.

so, I set topological rule "A must covered by B" on ArcInfo with setting 0.0001 as tolerance value. There was no error.

On QGIS, I implemented "Difference" from geoprocessing tool for two polygons.

I found hundred errors which has differences less than 0.001m.
As default, there is no tolerance value on QGIS.

Please tell me how to set tolerance value on QGIS if possible.

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You speak of topological rule, but QGIS is not yet a full topological GIS. You can examine all of the options in 2. Lesson: Feature Topology or How to check Topology in QGIS?

If you want a full topological GIS, use GRASS GIS

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