在Deactivate事件中，您可以取得NotifyIcon的Icon的Rectangle，然后检查它是否为Contains()的MousePosition，进而决定是否为Close()的MainForm。
我引用了这篇文章：How to obtain the icon rectangle of a NotifyIcon

internal static class NotifyIconExtensions
{
    //Works with Shell32.dll (version 6.1 or later)
    [DllImport("shell32.dll")]
    static extern int Shell_NotifyIconGetRect([In] ref NOTIFYICONIDENTIFIER identifier, [Out] out RECT iconLocation);

    [StructLayout(LayoutKind.Sequential)]
    struct RECT
    {
        public int Left;
        public int Top;
        public int Right;
        public int Bottom;
    }

    [StructLayout(LayoutKind.Sequential)]
    struct NOTIFYICONIDENTIFIER
    {
        public uint cbSize;
        public IntPtr hWnd;
        public uint uID;
        public Guid guidItem;
    }

    public static bool TryGetRectangle(this NotifyIcon notifyIcon, out Rectangle rectangle)
    {
        rectangle = Rectangle.Empty;

        var type = notifyIcon.GetType();

        var idFieldName = "id";
        var windowFieldName = "window";

        // Due to the difference in field names between .NET and .NET Framework,
        // it requires conditional checking.
        var fields = type.GetFields(BindingFlags.NonPublic | BindingFlags.Instance);
        if (!fields.Any(x => x.Name == idFieldName))
        {
            idFieldName = "_id";
            windowFieldName = "_window";
        }

        var idFieldInfo = type.GetField(idFieldName, BindingFlags.NonPublic | BindingFlags.Instance);
        if (idFieldInfo == null)
            return false;

        var iconId = (uint)idFieldInfo.GetValue(notifyIcon);

        var windowFieldInfo = type.GetField(windowFieldName, BindingFlags.NonPublic | BindingFlags.Instance);
        var nativeWindow = windowFieldInfo.GetValue(notifyIcon) as NativeWindow;
        if (nativeWindow == null)
            return false;

        var iconHandle = nativeWindow.Handle;

        var nid = new NOTIFYICONIDENTIFIER();
        nid.cbSize = (uint)Marshal.SizeOf(nid);
        nid.hWnd = iconHandle;
        nid.uID = iconId;

        int result = Shell_NotifyIconGetRect(ref nid, out var rect);

        if (result != 0)
            return false;

        rectangle = new Rectangle(rect.Left, rect.Top, rect.Right - rect.Left, rect.Bottom - rect.Top);
        return true;
    }
}

// in MainForm
protected override void OnDeactivate(EventArgs e)
{
    if (Program.notifyIcon.TryGetRectangle(out Rectangle rect))
    {
        Debug.WriteLine("{0}, {1}", MousePosition, rect);

        if (rect.Contains(MousePosition))
            return;
    }

    Close();
}

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这将引起另一个问题：当用户点击NotifyIcon触发MainForm的Deactivate事件后，如果点击其他窗口，则不会再触发MainForm的Deactivate事件。