Background The type of suture used in periodontal surgery can affect post-surgical complications. This study aimed to compare simple with cross-mattress sutures for nondisplaced flaps of the maxillary molar region. Methods This randomized controlled trial included 32 candidates of nondisplaced flap surgery of the maxillary molar region referred to the private office of a periodontist in Bandar Abbas, Iran from January 21 to May 4, 2020. First, the patients’ age, sex, and plaque index were recorded. Then, they were randomized into two equal groups. In the first group, the interdental suturing was done using simple sutures with 4–0 vicryl threads, and in the second group, interdental suturing was performed using cross-mattress sutures with the same threads. The primary outcome was suture time, including the duration of the first suture and the total duration of all sutures. The secondary outcomes were bleeding on probing and the requirement of supplementary sutures immediately after the surgery, as well as the gingival index (at suture removal and one month after surgery). Results The two groups were comparable regarding age, sex, and plaque index. The first suture duration was significantly longer in the simple group compared to the cross-mattress group (P < 0.001); however, the total suture time did not differ between groups. Moreover, a significantly higher number of patients in the simple group required supplementary sutures (50% vs. 6.3%, P = 0.006). There was no significant difference between groups regarding bleeding on probing and gingival index (at suture removal and one month after surgery). Conclusions Cross-mattress sutures were superior to simple sutures in terms of supplementary suture requirement for nondisplaced flaps of the maxillary molar region, while the two suturing techniques were alike regarding total suture time, gingival index, and probing on bleeding. Trial registration Iranian Registry of Clinical Trials (IRCT), IRCT20191224045882N1. Registered 08/02/2020. Registered while recruiting, https://www.irct.ir/trial/44754.