This paper deals with system engineering and design methodology for super low altitude satellites in the view of the computational mission analysis. Due to the slight advance of imaging instruments, such as the focus of camera and the image element of charge coupled device (CCD), it is an innovative and economical way to improve the camera’s resolution to enforce the satellite to fly on the lower altitude orbit. DFH-3, the mature satellite bus developed by Chinese Academy of Space Technology, is employed to define the mass and power budgets for the computational mission analysis and the detailed engineering design for super low altitude satellites. An effective iterative algorithm is proposed to solve the ergodic representation of feasible mass and power budgets at the flight altitude under constraints. Besides, boundaries of mass or power exist for every altitude, where the upper boundary is derived from the maximum power, while the minimum thrust force holds the lower boundary before the power reaching the initial value. What’s more, an analytical algorithm is employed to numerically investigate the coverage percentage over the altitude, so that the nominal altitude could be selected from all the feasible altitudes based on both the mass and power budgets and the repetitive ground traces. The local time at the descending node is chosen for the nominal sun-synchronous orbit based on the average evaluation function. After determining the key orbital elements based on the computational mission analysis, the detailed engineering design on the configuration and other subsystems, like power, telemetry telecontrol and communication (TT&C), and attitude determination and control system (ADCS), is performed based on the benchmark bus, besides, some improvements to the bus are also implemented to accommodate the flight at a super low altitude. Two operation strategies, drag-free closed-loop mode and on/off open-loop mode, are presented to maintain the satellite’s altitude. Finally, a flight planning schedule for the satellite is demonstrated from its launch into the initial altitude at the very beginning to its decay to death in the end.