The Hamiltonian dynamic model of distributed satellite system(DSS)relative motion under earth oblateness perturbation was introduced, and the Hamilton's equation of DSS relative motion was also obtained. Aiming at solving relative two-point boundary value problems of DSS under earth oblateness perturbation, a shooting method based on solving generating function was proposed. High precision formation adjusting problems of DSS under earth oblateness perturbation was calculated. Results demonstrate that the algorithm has high computational efficiency and can avoid the problem of dimension disaster.