Port throughput, as an indicator reflecting port scale, is associated with the port–city’s population base. By establishing an allometric growth model between the two, we can well verify the delicate relationship between port throughput and urban population. This article takes the throughput of Shanghai port and the population of Shanghai city as an example and studies the relative growth rate ratio between the two, that is, the scaling exponent b. In this example, the exponent b = 0.58 which is smaller than the theoretical value of 0.85, suggesting the improper development relationship between the two for the current phase. Shanghai urban population tends to be saturated, with the growth rate slowing down, and the contribution of urban population to port throughput decreasing. If this development trend proceeds for long, Shanghai port growth scale will be severely restricted. Apart from quantitative research on the relationship between the development rates of Shanghai port throughput and Shanghai urban population, this article also uses the Logistic model to forecast Shanghai port throughput and Shanghai urban population in the future to develop a scientific plan for Shanghai port scale so that port and city can achieve coordinated development.