The present investigation aims at analysing the effects of surface roughness (three possible types of roughness: isometric, longitudinal and transverse orientation of asperities) on lubrication mechanism at the coning gap which is formed between flexspline cup and cam interface in strain wave gear during assembly of its components. Investigation is further extended to analyse the effects of roughness on lubrication characteristics such as fluid flow speed, fluid flow force and fluid frictional force. In the present investigation at first, generalized Reynolds equation for hydrodynamic lubrication is modified to make it suitable for coning gap and then, micro-polar terms as well as surface roughness terms for all possible roughness (isometric, longitudinal and transverse) are incorporated into it. Conservative form of finite difference method is applied to solve the all three complicated Reynolds equation under suitable boundary conditions. The solution of Reynolds equation is further utilized to derive the lubrication characteristics like fluid flow speed, fluid flow force and fluid frictional force. Methods of finding lubrication pressure profiles and lubrication characteristics under micro-polar fluid with surface roughness are established. Effects of roughness terms on pressure profiles as well as on lubrication characteristics are also established. All analyses are done in dimensionless form. Originality of present investigation is lubrication analysis at the coning gap of strain wave gear under rough surfaces and the finding effects of roughness on it. © 2021 Author(s).