protected void Page_Load(object sender, EventArgs e)
{
    String[] files = @"C:\ENROLLDOCS\A1.pdf,C:\ENROLLDOCS\A2.pdf".Split(',');
    MergeFiles(@"C:\ENROLLDOCS\New1.pdf", files);
}
public void MergeFiles(string destinationFile, string[] sourceFiles)
{
    if (System.IO.File.Exists(destinationFile))
        System.IO.File.Delete(destinationFile);

    string[] sSrcFile;
    sSrcFile = new string[2];

    string[] arr = new string[2];
    for (int i = 0; i <= sourceFiles.Length - 1; i++)
    {
        if (sourceFiles[i] != null)
        {
            if (sourceFiles[i].Trim() != "")
                arr[i] = sourceFiles[i].ToString();
        }
    }

    if (arr != null)
    {
        sSrcFile = new string[2];

        for (int ic = 0; ic <= arr.Length - 1; ic++)
        {
            sSrcFile[ic] = arr[ic].ToString();
        }
    }
    try
    {
        int f = 0;

        PdfReader reader = new PdfReader(sSrcFile[f]);
        int n = reader.NumberOfPages;
        Response.Write("There are " + n + " pages in the original file.");
        Document document = new Document(PageSize.A4);

        PdfWriter writer = PdfWriter.GetInstance(document, new FileStream(destinationFile, FileMode.Create));

        document.Open();
        PdfContentByte cb = writer.DirectContent;
        PdfImportedPage page;

        int rotation;
        while (f < sSrcFile.Length)
        {
            int i = 0;
            while (i < n)
            {
                i++;

                document.SetPageSize(PageSize.A4);
                document.NewPage();
                page = writer.GetImportedPage(reader, i);

                rotation = reader.GetPageRotation(i);
                if (rotation == 90 || rotation == 270)
                {
                    cb.AddTemplate(page, 0, -1f, 1f, 0, 0, reader.GetPageSizeWithRotation(i).Height);
                }
                else
                {
                    cb.AddTemplate(page, 1f, 0, 0, 1f, 0, 0);
                }
                Response.Write("\n Processed page " + i);
            }

            f++;
            if (f < sSrcFile.Length)
            {
                reader = new PdfReader(sSrcFile[f]);
                n = reader.NumberOfPages;
                Response.Write("There are " + n + " pages in the original file.");
            }
        }
        Response.Write("Success");
        document.Close();
    }
    catch (Exception e)
    {
        Response.Write(e.Message);
    }
}

source