<!-- This is the code you provided -->
<td><input type="text" name="option" onkeydown="random()" class="form-control"  >

<script>
            function random()
            {
                
                var a=document.getElementById('option').value;
                if(a==="red")
                {
                    var minimum = '5';
                }
                else if(a==="green")
                {
                    var minimum= '10';
                }
                    
            }
       </script>
       <input type="NUMBER" name="qty"  class="form-control" min=<?php var minimum ?>  ></td>

Let's see... First of all lets change your if else case with a switch:

switch(a){
    case "red":
        var minimum = 5;
        break;
    case "green":
        var minimum = 10;
        break;
}

Now I will remove the php tag and add a line to change the min value of the input.

<td><input type="text" id="option" onkeydown="random()" class="form-control"  />

<script>
            function random()
            {
                var a=document.getElementById('option').value;
                switch(a){
                    case "red":
                        var minimum = 5;
                        break;
                    case "green":
                        var minimum = 10;
                        break;
                }
                document.getElementById("input").setAttribute("min", minimum)//this line adds an attribute or sets it to a given value
            }
       </script>
       <input type="NUMBER" id="input"  class="form-control" /></td>

Now let's see this code in action! Run the following snippet.

<td><input type="text" id="option" onchange="random()" class="form-control"  />

<script>
            function random()
            {
                var a=document.getElementById('option').value;
                switch(a){
                    case "red":
                        var minimum = 5;
                        break;
                    case "green":
                        var minimum = 10;
                        break;
                }
                document.getElementById("input").setAttribute("min", minimum)//this line adds an attribute or sets it to a given value
            }
       </script>
       <input type="NUMBER" id="input"  class="form-control" /></td>

And done! Also, I changed the onkeydown to onchange.

1. Added more rows in case there are many rows with the same fields.
2. Secondly, I have added an event listener instead of direct function call but you can do either.
3. Extracting into calculatingMinimunQuantity for easier readibility and calling setAttribute (min) there.

var options = document.querySelectorAll(".option");
options.forEach(function(option) {
  option.addEventListener("change", function() {
    calculatingMinimunQuantity(option);
  });
});

function calculatingMinimunQuantity(option) {
  var minimum = 0;
  var value = option.value;
  if (value === "red") {
    minimum = "5";
  } else if (value === "green") {
    minimum = "10";
  }
  //   getting the quantity input field
  option.nextElementSibling.setAttribute("min", minimum);
}

<td>
  <div>
    <input type="text" class="option form-control" placeholder="option" name="option" />
    <input type="NUMBER" class="form-control" name="qty" placeholder="quantity" />
  </div>
</td>

<td>
  <div>
    <input type="text" class="option form-control" placeholder="option" name="option" />
    <input type="NUMBER" class="form-control" name="qty" placeholder="quantity" />
  </div>
</td>