Background: A great deal of research suggests that arthroscopic ankle fusion (AAF) has advantages over open ankle fusion (OAF), but these outcomes would be imprecise because of a selection bias. The purpose of this study is to verify which is better for ankle fusion, AAF or OAF. We regrouped the OAF group into two subgroups according to whether the osseous operation type is the same as AAF group. The goal is to minimize the impact of disease severity, thereby reducing selection bias to some extent. Methods: We retrospectively analyzed the data of ankle fusion in our hospital between July 2015 and October 2018. Forty-three patients were enrolled and divided into AAF group (n = 17) and OAF group (n = 26). In order to eliminate selection bias, we divided OAF group into complex osseous operation subgroup (COO subgroup) (n = 15) and simple osseous operation subgroup (SOO subgroup) (n = 11). The osseous operation type of SOO subgroup is the same as AAF group. Then, we compared the differences between these groups. All patients were followed up at least 1 year after operation. We analyzed data, including etiology composition, surgical time, intra-op blood loss, reduction of albumin, total hospital stays, union time, fusion situation, complications, radiological examination, functional score, and questionnaire survey. Then we performed statistical analyses. Results: We found that the etiological components of AAF group and OAF group were different; the etiological components of AAF group and SOO subgroup were similar. We found that AAF group has advantages over OAF group and COO subgroup in general. However, except in terms of surgical trauma, hospital stays, and short-term complications occurred, the AAF group has not obvious advantages over SOO subgroup, including intra-op blood loss, fusion condition, postoperative function score, and postoperative patient satisfaction; and AAF group need more surgical time than the SOO subgroup. Conclusions: The arthroscopic ankle fusion can bring a good curative effect; however, if the osseous operation type is the same, the arthroscopic ankle fusion only has a limited advantage over the traditional open operation in perioperative soft tissue protection and enhanced recovery after surgery.