The invention discloses a shallow-earthing, large-section and small-distance construction method for a rectangular pipe jacking overpass subway tunnel and relates to the field of pipe jacking construction. The method comprises the steps that firstly, the weight of soil planed to be excavated is calculated according to the reconnaissance report result, meanwhile, the weight of a concrete pipe joint is calculated, the number of applied balance weights is estimated according to the difference between the weight of the soil and the weight of the concrete pipe joint, and corresponding concrete balance weights are prepared; the deformation condition of the lower subway tunnel is monitored in real time during pipe jacking tunneling, when protruding deformation is approximate to an early warning value, the balance weights are started to be applied in a pipe jacking channel, and meanwhile deformation of the subway tunnel continues to be monitored; along with further advancing of the pipe jacking tunnel, the positions of the originally applied balance weights are kept unchanged, according to the actually measured protruding deformation value of the subway tunnel, when the protruding deformation is approximate to the early warning value, the balance weights are started to be applied to the position, corresponding to the maximum protruding deformation, in the pipe jacking channel; after all the pipe jacking construction is completed, the balance weights are withdrawn step by step. The technical aim that under the condition that grouting reinforcement, open cutting, water lowering and other measures cannot be taken, when the subway tunnel is operated in the mode of shallow underground excavation large-section rectangular pipe jacking close-range upward penetrating, the protruding deformation of the lower subway tunnel is controlled is achieved.