This paper presents design and implementation of a super twisting sliding mode control for superheat temperature and evaporating temperature of refrigerant fluid in an evaporator of HVAC (Heating-Ventilation and Air Conditioning)-Refrigeration system. Based on a nonlinear model of the evaporator two control approaches are presented. The first approach is based on a Multi-Input Multi Output (MIMO) system in which there are two control inputs; inlet mass flow and outlet mass flow rate, and the outputs are the length of two phase flow and evaporating temperature of refrigerant. The second approach considers the system as a Single input single output (SISO) one, and by using inlet mass flow, superheat temperature is controlled. In the first approach, by implementing a feedback linearization method the two control inputs are decoupled. By decoupling the effects of both inputs, the two state variables of system are controlled separately and effectively. By applying sliding mode control robustness against the disturbances and uncertainties is guaranteed. Super-twisting algorithm is applied as a remedy for chattering problem in classical sliding mode control and achieving finite time convergence. Controller and model of systems are simulated using MATLAB and Simulink. The results of simulations show the effectiveness of designed controller in presence of uncertainties.