import arcpy
mxd = arcpy.mapping.MapDocument("path to mxd")
lyr = arcpy.mapping.ListLayers(mxd, "layer name")[0]
arcpy.SelectLayerByAttribute_management(lyr, "NEW_SELECTION", "some query")
mxd.save()
#If you don't want to save the selection to the existing MXD, try saving it to another file:
mxd.saveACopy("path to new MXD")