We introduce and define for the first time the concept of a non-homogeneous Markov system in a stochastic environment (S-NHMS). The problem of finding the expected population structure in an S-NHMS is studied, and important properties among the basic parameters of the S-NHMS are established. Moreover, we study the problem of maintaining the relative sizes of the states in a stochastic environment applying control in the input process. Among other things, we provide the probability of maintaining any vector of relative state sizes. Also strategies for attaining in an optimal way a desired relative structure are designed, with the use of a given algorithm. Finally, an illustration is provided of the present results in a manpower system.