In the future Space Information Network (SIN), remote sensing satellites (RSSs) can access communication constellations (CC) and ground stations (GSs) through inter-layer links (ILLs) and satellite-ground links (SGLs) to realize the timely transmission of large amounts of observation data. In this paper, we study the link topology of both ILLs and SGLs with different time slot durations from the perspective of each RSS based on the time-expanded graph. We propose a multi-objective mission flow optimization model to jointly achieve transmission benefits maximization, end-of-period energy maximization, and transmission wait time minimization. This model considers missions’ importance differences under limited storage, energy, and link bandwidth resources. To reduce the solving complexity, we propose a Phased Multi-Objective (PMO) algorithm composed of two Integer Linear Programming (ILP) problems and one Linear Programming (LP) problem to separate the integer programming part from the continuous part. A Multi-Objective Mixed Integer Linear Programming (MO-MILP) model is also formulated for comparison. We simulate the proposed methods in different scale SIN with practical parameters referred to the SAR satellites. The results indicate that observation data can be transmitted in near real-time with adequate bandwidth of ILLs. PMO can achieve multiple objectives and is applicable in large-scale constellation systems.