JavaScript alert boxes can be combined with PHP to display messages to the user based on server-side logic. One way to do this is to use PHP to generate JavaScript code that displays the alert box when certain conditions are met.

Here’s an example of how you can use PHP and JavaScript to display an alert box when a form is submitted:

<?php
if ($_SERVER['REQUEST_METHOD'] == 'POST') {
  // process form data

  if ($form_data_is_valid) {
    // form data is valid, show success message
    $message = "Form submitted successfully!";
    echo "<script>alert('$message');</script>";
  } else {
    // form data is invalid, show error message
    $message = "Form data is invalid.";
    echo "<script>alert('$message');</script>";
  }
}
?>

<!-- HTML form -->
<form method="post">
  <!-- form fields go here -->
  <input type="submit" value="Submit">
</form>

In this example, the PHP code checks whether the form has been submitted and whether the form data is valid. If the form data is valid, it generates a JavaScript code that displays an alert box with a success message. If the form data is invalid, it generates a JavaScript code that displays an alert box with an error message.

Note that the $message variable is escaped with single quotes to prevent JavaScript injection attacks. This ensures that the message is properly encoded and does not contain any special characters that could be interpreted as JavaScript code.

Also note that using alert() to display messages to the user is not always the best option, as it can disrupt the user experience and can be blocked by certain browser extensions. It is often better to use other user-friendly methods to display messages, such as a toast notification or a modal dialog box.