The paper presents the identification issues and the parameters identification algorithm that separates the system parameters from the time delays for a class of multi-input single-output (MISO) linear time delay systems (LTDS). The presence of the unknown time delay greatly complicates the parameter estimation problem, because the parameters of the model are not linear with respect to the time-delay in terms of the identification. This problem for SISO systems is solved in the papers [6] and [7]. Solution presented in the previous mentioned paper is based on the nonlinear least square problem developed in the paper [1]. In this paper, the approach worked out in the papers [6] and [7] is extended to the class of MISO systems. The multipoint search method based on the Quasi-Newton technique is used for the minimization of variable projection functional. The special Quasi-Newton algorithm, which involves the several initial conditions treated at the same time, developed in [5], is applied here. This approach is illustrated by a particular application in the field of the heat transfer, on the time-delay model of the heat exchanger in the laboratory environment.