感谢@howlger提到的答案，我修改了我的代码，如下所示，使我的pdf可以从eclipse和JAR访问。

public static void openUserManual() {
        File userManual;
        try {
            userManual = new File(Global.class.getResource("/cct/resources/manual.pdf").toURI());
            Desktop.getDesktop().open(userManual); // works when run from eclipse
        }
        catch (Exception ex) {
            try {
                userManual = getResourceAsFile(Global.class.getResource("/cct/resources/manual.pdf").getPath());
                if (userManual != null)
                    Desktop.getDesktop().open(userManual); // works when run from JAR
                else
                    JOptionPane.showMessageDialog(null, "User Manual couldn't be accessed.");
            }
            catch (Exception exp) { exp.printStackTrace(); }
        }
    }
    
    private static File getResourceAsFile(String resourcePath) {
        try (InputStream in = Global.class.getResourceAsStream(resourcePath)) {
            if (in == null)
                return null;

            File tempFile = File.createTempFile(String.valueOf(in.hashCode()), ".tmp");
            tempFile.deleteOnExit();

            try (FileOutputStream out = new FileOutputStream(tempFile)) {
                //copy stream
                byte[] buffer = new byte[1024];
                int bytesRead;
                while ((bytesRead = in.read(buffer)) != -1)
                    out.write(buffer, 0, bytesRead);
            }
            return tempFile;
        } catch (IOException exp) { exp.printStackTrace(); return null; }
    }