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The paper discusses the effect of non-smooth dead-zone (NDZ), and input actuator misalignment (AMA) during spacecraft attitude tracking maneuver in presence of parametric uncertainties and external perturbations. Initially, the input AMA and NDZ models are formulated to transform spacecraft attitude model dynamics. Subsequently, a new second order disturbance observer (SODO) is devised to get the total disturbance. The observer is developed considering system perturbations as extended states, with an additional term Introduced to improve the observer performance. Finally, a distinctive integral sliding mode control (ISMC) law is developed and integrated with the proposed SODO to perform spacecraft attitude control operations. Comparative simulations are conducted on the spacecraft attitude control model with input AMA, NDZ, system parametric uncertainties and external disturbances to show the effectiveness of the proposed control structure. • A novel SODO-SMC control law is proposed in this work to attain precise attitude tracking of spacecraft subject to input AMA, NDZ, parameter uncertainty, and external disturbance. • The entire system perturbation is estimated via a new SODO. The proposed SODO improves performance with a corrective function. • An input AMA model for spacecraft attitude control is developed, considering the system fully-actuated. [ABSTRACT FROM AUTHOR]