I am trying to change Panel height, then irfame alignment is getting out.

Refer link your

Using multiple Ajax ModalPopupExtender on same page in ASP.Net

<asp:Panel ID="Panel4" runat="server" Height="400"   CssClass="Popup" align="center" Style="display: none">
    <asp:Button ID="Button1" runat="server" Text="Close" />
    <iframe  id="Iframe1" width="550" height="200" src="partycrdt.aspx" runat="server"></iframe>
    <br />
</asp:Panel>

I used two iframe on one page, one Pop Window size is big and second popup window size is small

<style type="text/css">
    .Background
    {
        background-color: Black;
        filter: alpha(opacity=90);
        opacity: 0.7;
    }  
    .Popup
    {
        background-color: #FFFFFF;
        align-items: flex-start;
        border-width: 3px;
        border-style: solid;
        border-color: black;
        padding-top: 400px;
        padding-left: 0px;
        width: 1100px;
        height: 1600px;
    }
    .lbl
    {
        font-size:16px;
        font-style:italic;
        font-weight:bold;
    }
</style>