In this paper, a thick mesoporous silica film (MSF) (more than 700 nm) was fabricated via the two-step enhancing Stöber solution growth approach (ESSGA). According to the optimization based on the transfer matrix method, a thicker MSF sensor has higher waveguide index sensitivity and is more suitable for the adsorbent detection, while a thinner MSF sensor has higher covered medium index sensitivity and is more appropriate for non-adsorbent detection. The covered medium index sensitivity and refractive index resolution of the fabricated MSF optical waveguide sensor were calculated to be 53.18 deg/RIU and ${1.28}\; \times \;{{10}^{ - 6}}\;{\rm RIU}$1.28×10-6RIU, respectively. For the detection of a small molecule, hexadecyltrimethylammonium bromide was used as a model of a small molecule to verify its sensing property and its limit of detection (LOD) as low as 1.879 nM was obtained. In order to detect heavy metal ions, the MSF was modified with an amino group by the post-grafted method. The response of the resonance angle shift is more sensitive to ${{\rm Pb}^{2 + }}$Pb2+ ion than ${{\rm Cu}^{2 + }}$Cu2+ ion and both their LODs could reach the nanomolar detection level; those are 17.30 and 6.44 nM, respectively.