There are a few possible ways of doing it in Matlab.
To make sure we are on the same page: you want to test if there is a significant difference in means of two signals (time series represented as vectors) ?
Assuming so and If the signal values conform to normal distribution you can compute a parametric test using the following function (with settings depending on the nature of your data, look up documentation): ttest2 (two-sample t-test; part of statistical toolbox), e.g.
[h,p,ci,stats] = ttest2(sig1,sig2); with 2 signal vectors
You can also do a non-parametric test (again stat toolbox required), such as Kolmogorov-Smirnov: kstest2 with the similar syntax as for t-test .