<p>In the future Space Information Network (SIN), mission satellites can be users to access communication constellations and ground stations through inter-layer links (ILLs) and satellite-ground links (SGLs) to realize the timely transmission and utilization of mission data. In this paper, we study the link topology of both ILLs and SGLs with different time-slot duration from the perspective of each user satellite based on the time-expanded graph. We propose a mission flow optimization model under limited onboard storage, energy, and link load resources. The model aims to jointly realize the maximization of data transmission benefits, the maximization of end-of-period energy, and the minimization of transmission wait time with the consideration of mission importance differences. We propose a Phased Multi-Objective (PMO) algorithm composed of two Integer Linear Programming (ILP) problems and one Linear Programming (LP) problem to reduce complexity by separating the integer programming part from the continuous part. Simulation is executed in an SIN with 66 communications satellites, 70 user satellites, and 5 ground stations. Compared to directly solving the integrated Mixed Integer Linear Programming (MILP) problem, the results show that PMO can significantly reduce the solution time and obtain an optimal solution close to MILP.</p>