3D endoscopes are utilized for fast and accurate cancer diagnosis and treatment by additionally providing depth and morphological information of target tissues compared to conventional 2D endoscopes. However, realization of 3D measurement module in small-sized and flexible endoscopes is having difficulties because of the additional required space and complexity of optical components for 3D imaging. Recently, miniaturization of optical equipment has been possible due to miniaturized optical components and image sensors, fabricated by the development of MEMS technology. This study presents miniaturized periodic micro optics designed and manufactured by MEMS fabrication technology for the realization of single image sensor based 3D flexible medical endoscope. Real-time 3D stereoscopic medical endoscope prototype was proposed with the symmetric microprism arrays based camera module, while flexible medical endoscope prototype with quantitative 3D imaging was also proposed with rotational offset microlens arrays based structured light/illumination switching module. The verification of 3D quantitative measurement of both proposed 3D endoscope prototypes was conducted by reconstructing the 3D depth map with single camera based calculation. The proposed periodic micro optics will provide a new direction for the miniaturized optical imaging systems with 3D measurement function such as medical endoscopes, smartphones, and drones.