In this paper, silicon-based micro and subwavelength optical elements based on a free-standing silicon nitride (SiNx) membrane are achieved. These elements, including gratings, microlenses, and holographic optical elements (HOEs), are designed and used within the visible and infrared regions. These devices can be used as collimators, reflectors, and wavelength-dependent filters with advantages of simple structure, high efficiency and feasibility to integrate with other elements into a micro-system chip. In order to demonstrate the advantage of micro-optics of free-standing SiNx membrane type in integration, a miniaturized optical pickup head module based on a stacked micro-optical system is developed. This module consisted of a laser diode, a reflector, a grating, a holographic optical element, and some aspherical Fresnel lenses. The novel microoptical system can overcome the problems encountered in other microoptical systems such as off-axis aberration, lower optical efficiency or durability, integration and even in fabrication. A focal spot with a FWHM diameter of 3.3 μm is obtained while the diffraction limited full-width at half-maximum (FWHM) is 0.7 μm. To extend the advantage of micro-optics of free-standing SiNx membrane, the subwavelength optical elements base on guided-mode resonance is also developed. With various Si-based structures, the filter possesses numerous properties such as variable bandwidths, low sideband, flattop, and etc. They are also applied as biosensors to detect the hybridization process of bio reaction for their high sensitivity. The results show that micro and subwavelength optical elements fabricated on Si-based material will be a candidate for emerging silicon micro-photonics.