如果不想修改input的width，可以flex#fields容器并指定flex-direction: column;。

setInterval(function() {
  var input = '<input type="text">';
  $("#fields").append(input);

}, 2000);

body {
  background: grey;
  display: flex;
  align-items: center;
  justify-content: center;
}

#fields {
  display: flex;
  flex-direction: column;
  background: green;
  padding: 20px;
}

#fields input {
  width: 100%;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<div id="fields">
  <input type="text">
</div>

使用display: block代替width: 100%：

setInterval(function() {
  var input = '<input type="text">';
  $("#fields").append(input);

}, 2000);

body {
  background: grey;
  display: flex;
  align-items: center;
  justify-content: center;
}

#fields {
  background: green;
  padding: 20px;
}

#fields input {
  display: block;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<div id="fields">
  <input type="text">
</div>

setInterval(function() {
  var input = '<input type="text">';
  $("#fields").append("<br>"+input);

}, 2000);

body {
  background: grey;  
}

#fields {
  background: green;
  padding: 20px;  
  text-align:center;
}


#container{
width:60%;
border:solid 2px green;
margin:0 auto;
}

<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
<div id='container'>
<div id="fields">
  <input type="text">
</div>
</div>