preventDefault()

HTML

<div id="popUpmain">
        <form action="">
            <div id="popUp" style="display:none">
                <h1 class="popUp-heading">Sign Up</h1>
                <input type="text" class="pop-up-name" placeholder="Your Name">
                <input type="text" class="pop-up-email" placeholder="Email">
                <input type="text" class="pop-up-number" placeholder="Number">
                <select name="Select Product" id="" class="popup-select">
                    <option value="Select Product active">Select Product</option>
                    <option value="Mattress">Mattress</option>
                    <option value="Select Product active">Comforter</option>
                    <option value="Select Product active">pillow</option>
                </select> 
                <input type="submit" class="popup-btn close-popup">
                <button class="close-btn close-popup">Not Now</button>
            </div>
        </form>
    </div>

JavaScript

$(document).ready(function(){
  setTimeout(function(){
    $('#popUp').css('display','block'); }, 3000
  );
}); 

$('.close-popup').click(function(e){
  e.preventDefault();
  $('#popUp').css('display','none');
});