When the endoscopic Achilles tendon repair technique is utilized, direct stitching of the ruptured site is challenging due to the frayed tendon stumps. To explore whether undesirable coaptation of the tendon stumps influences the generation of the tendons. This study is a retrospective analysis of 46 patients who underwent a modified endoscopic Achilles tendon rupture repair from October 2018 to June 2020. Patients were divided into two groups according to the coaptation of tendon stumps on postoperative ultrasonography. Group 1 included 17 cases with undesirable coaptation (<50%), and Group 2 included 29 cases with appropriate coaptation (≥50%). Magnetic resonance imaging (MRI) was obtained postoperatively at 3, 6, and 12 months to evaluate the tendon morphological construction. Clinical evaluations were performed using the American Orthopedic Foot and Ankle Society (AOFAS) ankle-hind foot score, the Achilles Tendon Total Rupture Score (ATRS), muscle power, and the Achilles tendon resting angle at the final follow-up. Complications were also encountered. The Student's t-test and the Mann-Whitney U-test were used to assess differences among both groups. The mean follow-up time was 37.5 ± 10.6 months in Group 1 and 39.0 ± 11.6 months in Group 2, respectively. The average age in Group 1 is slightly older than in Group 2 (37.3 ± 6.1 vs. 32.7 ± 6.3, p = 0.021). The tendon cross-section areas and thickness increased initially and decreased later on postoperative MRI evaluation. It also showed a significantly higher signal/noise quotient (SNQ) in Group 1 at postoperative 3 months. At postoperative 6 and 12 months, the SNQ between both groups was similar. The AOFAS score (95.9 ± 5.1 vs. 96.2 ± 4.9, p = 0.832), ATRS score (97.0 ± 3.6 vs. 97.7 ± 3.3, p = 0.527), and muscle power (21.38 vs. 24.74, p = 0.287) were not significantly different between both groups. However, the resting angle of Group 1 was significantly larger than that of Group 2 (4.6 ± 2.4 vs. 2.4 ± 2.3, p = 0.004). There was no difference in the complications (p = 0.628). Although complete regeneration can be finally achieved, the early stage of tendon stump regeneration can be prolonged due to undesirable coaptation when endoscopic Achilles tendon repair technique is applied. The prolonged high signal duration on MRI indicates the less-than-ideal regeneration of the tendon, which might lead to elongation of the tendon.