优化通常是减少io。
在您的情况下，减少sql查询的数量应该可以提高处理时间。
如果你需要处理大量的记录，你应该把它分割成块。每个区块应该包含一批可以放入内存（ram）的记录。
从数据库中检索块。处理块（即使用循环），并使用数组（ie）跟踪需要在db中执行的更改。最后，用尽可能少的查询批量更新数据库。

$data = $this->input->post();
       $project_id = $data['project_id'];

       $this->db->where('project_id', $project_id);
       $paper = $this->db->get('paper')->result();

       $paper2 = $paper; //duplica o array de papers
       $duplicatesCount = 0;

       // keep track of updates
       $updates = [];

       foreach($paper as $p){
           $similarity = null;

            foreach($paper2 as $p2){
                if($p -> status_selection_id !== 4 && $p2 -> status_selection_id !== 4){ 
                    if($p -> paper_id !== $p2 -> paper_id){ 
                        similar_text($p -> title, $p2 -> title, $similarity);

                        if ($similarity > 90) { 

                            $updates[] = [
                                'paper_id' => $p -> paper_id,
                                'status_selection_id' => 4,
                            ];

                            $duplicatesCount ++;
                        }
                    }
                }
            }
        }

        if ($duplicatesCount > 0) {
             // here you have to create a big SQL request with all the updates
             // maybe your DB adaptor can do it for you ?
             $query = $this->db->somethingToCreateABulkQuery();
             foreach ($updates as $update) {
                 // stuff 
                 $query->somethingToAddAndUpdate($update);
             }
             $this->db->somethingToExecuteTheQuery($query);

        }