This exercise of yours can be done in a few different ways.
(1) Store time steps (time array) along with the input data in a cell array, e.g. Data or initially specify time step size if known
(2) Employ sim() to run your Simulink model from MATLAB environment.
(3) In Simulink model, use [From WorkSpace] and [To WorkSpace] blocks, which are used to get the data from MATLAB workspace to simulate the model and send the results back to MATLAB workspace.
(4) In MATLAB code, use sim() to run the SImulink model within a loop. E.g.:
Data = ...
for ii = 1:1000
IN = Data{ii}; % Call [IN] for simulation using [From WorkSpace] block variable's name is IN
OUT{ii}= sim('M_Run.slx'); % Simulation results from the Simulink model M_Run.slx. All simulation results saved under the var name OUT
% Note OUT can be also save a a structure or an array as well)
end
