Grap.TranslateTransform(0, pictureBoxGraph.Height - 1);
                Grap.ScaleTransform(1, -1);

------------------------------- 
            if (IsDrawing && e.Button == MouseButtons.Left && !IsImgMove)
            {
                //将数据点存储以便画线
                _DrawLine.Add(new Point(e.X, e.Y));
            }

{
    Grap.TranslateTransform(0, pictureBoxGraph.Height - 1);
    Grap.ScaleTransform(1, -1);
    this.matrix = Grap.Transform;   // 得到转换矩阵
    this.matrix.Inverse();          // 得到逆转换
}

System.Drawing.Drawing2D.Matrix matrix = new Matrix();
void Form1_MouseDown(object sender, MouseEventArgs e)
{
    Point[] points = {e.Location};
    this.matrix.TransformPoints(points);  //<--
    this.Text = points[0].ToString();
}

------解决方案--------------------

Matrix Transform
看这个，http://nonocast.cn/?p=2835