Objective. To assess the clinical efficiency of endoscopy-assisted laparoscopic versus laparoscopic surgery for gastrointestinal stromal tumors and the impact on patients’ coagulation, surgical condition, and complications. Methods. Between November 2016 and May 2020, 126 eligible patients diagnosed with gastrointestinal stromal tumor (GIST) in our institution were recruited. They were concurrently randomly assigned at a ratio of 1 : 1 to receive either laparoscopic gastrectomy (reference group) or endoscopy-assisted laparoscopic gastrectomy (research group). The two groups were compared in terms of patients’ coagulation function, surgical conditions, and complications. Results. The two groups had similar preoperative coagulation indices and the postoperative levels of activated partial thromboplastin time (APTT) and thromboplastin time (TT) (
P
>
0.05
). Compared with the reference group, the research group showed lower PT levels (10.48 ± 0.68 vs. 11.97 ± 0.46) and higher FIB levels (0.67 ± 0.11 vs. 0.29 ± 0.07) (
P
<
0.05
). Compared with the reference group, the study group had shorter operative time (81.21 ± 10.24 min versus 98.98 ± 15.31 min), shorter surgical incision (3.63 ± 1.12 cm versus 5.01 ± 1.14 cm), and less intraoperative bleeding (18.74 ± 6.98 ml versus 58.69 ± 15.87 ml) (
P
<
0.05
). A markedly shorter length of hospital stay, time to the first postoperative exhaustion, and duration of drainage tube and gastric tube dwelling were observed in the research group versus the reference group (
P
<
0.05
). The study group presented higher nutritional levels of patients at 3 days after surgery and a lower incidence of complication. Conclusion. Endoscopy-assisted laparoscopic treatment shows significant improvements in the efficiency of minimally invasive surgery and ensures a better prognosis and quality of life of patients with a good safety profile, so it is worthy of clinical application.