This paper proposes a class of hierarchical population model, in form of nonlinear system of difference equations, and studies several control problems, including controllability, stabilization and optimal harvesting. The upper and lower controllability are proven by a corresponding result of suitable linear systems and the comparison principle, and the associated control strategies are constructed. On the other hand, the exact controllability of the population system is established by means of frozen coefficients, linear controllability and the Kakutani fixed point theorem of set-valued maps. The stabilization result follows from the linearization around zero solution and its controllability. Furthermore, a kind of optimal harvesting problems are investigated. General policy is carefully described and, in three special cases, concrete results are obtained. Finally, the effects of individuals economic values on harvesting efforts are examined by a numerical approach.