Spin dependent quantum transport properties in twisted carbon nanotube and stretched carbon nanotube are calculated using density functional theory (DFT) and non-equilibrium green’s function (NEGF) formulation. Twisting and stretching have no effect on spin transport in CNTs at low bias voltages. However, at high bias voltages the effects are significant. Stretching restricts any spin-up current in antiparallel configuration (APC) which results in higher magneto resistance (MR). Twisting allows spin-up current almost equivalent to the pristine CNT case resulting in lower MR. High spin filtration is observed in PC and APC for pristine, stretched and twisted structures at all applied voltages. In APC, at low voltages spin filtration in stretched CNT is higher than in pristine and twisted ones with pristine giving higher spin filtration than twisted CNT.