<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with Wdesk from Workiva-->
<!--Copyright 2020 Workiva-->
<!--r:ce8061dd-ff9f-48a6-b8ce-df30f4b611e1,g:90313321-ad23-450f-8f87-03005c1479ad-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.codexis.com/role/Cover" xlink:type="simple" xlink:href="cdxs-20201105.xsd#Cover"/>
  <link:calculationLink xlink:role="http://www.codexis.com/role/Cover" xlink:type="extended"/>
</link:linkbase>
