1、三类医疗器械经营许可证办理方式如下：
（1）申请人提交申请资料到相关部门；
（2）相关部门受理申请人的申请；
（3）到实际场地进行勘察以及对产品进行审核；
（4）准予颁发三类医疗器械许可证。
2、法律依据：《医疗器械监督管理条例》第十四条
第一类医疗器械产品备案和申请第二类、第三类医疗器械产品注册，应当提交下列资料：
（一）产品风险分析资料；
（二）产品技术要求；
（三）产品检验报告；
（四）临床评价资料；
（五）产品说明书以及标签样稿；
（六）与产品研制、生产有关的质量管理体系文件；
（七）证明产品安全、有效所需的其他资料。4、工商行政管理部门出具的《企办理三类医疗器械经营许可证的办理流程：
1.向食品药品监督管理局提交医疗器械经营许可证申请材料；
2.食品药品监督管理局数据形式审查；
3.数据正式受理；
4.有关部门的行政审查；
5.现场评价；

egal basis: Article 14 of the Regulations on Supervision and Administration of Medical Devices for the filing of Class I medical devices and application for the registration of Class II and III medical devices shall submit the following materials: (1) product risk analysis data; (2) technical requirements (3) product; (3) product inspection report; (4) clinical evaluation data; (5) product instructions and label samples; (6) quality management system documents related to product development and production; (7) other materials required to prove the safety and effectiveness of the product. 4. Procedures for handling third III medical device business license issued by the industrial and commercial administration: 1. Submit application materials for medical device business license to the Food and Drug Administration; 2. Data form review of the Food and Drug Administration; 3. Official acceptance of data; 4. Administrative review of relevant departments; 5. On-site evaluation;