I finally found the solution. I want to write it in case someone else needs it. When canonicalizing a sub node, you have to add parent nodes namespaces. It does not matter if you use it in the related sub node or not. Therefore, before canonicalizing the element, I added the namespaces belong to parent nodes to my XmlElement.

public static string Canonicalize(XmlElement Element)
{
    //Create [NamespaceList]
    #region

    var NamespaceList = new Dictionary<string, string>();
    ModifyNamespaceList(Element, ref NamespaceList);

    #endregion

    foreach (var Namespace in NamespaceList)
    {
        Element.SetAttribute(Namespace.Key, Namespace.Value);
    }

    var ElementStream = new MemoryStream();
    var ElementWrtier = XmlWriter.Create(ElementStream);
    Element.WriteTo(ElementWrtier);
    ElementWrtier.Flush();
    ElementStream.Position = 0;

    var c14n = new XmlDsigC14NTransform(false);
    c14n.LoadInput(ElementStream);

    using (var OutStream = (Stream)c14n.GetOutput(typeof(Stream)))
    using (var OutStreamReader = new StreamReader(OutStream, Encoding.UTF8))
    {
        return OutStreamReader.ReadToEnd();
    }
}

private static void ModifyNamespaceList(XmlNode Node, ref Dictionary<string, string> NamespaceList)
{
    if (Node.Attributes != null)
    {
        foreach (XmlAttribute item in Node.Attributes)
        {
            if (item.Prefix == "xmlns" || item.Name == "xmlns")
            {
                if (!NamespaceList.TryGetValue(item.Name, out string Value))
                {
                    NamespaceList.Add(item.Name, item.Value);
                }
            }
        }
    }

    if (Node.ParentNode != null)
    {
        ModifyNamespaceList(Node.ParentNode, ref NamespaceList);
    }
}