Global mean sea surface temperature (SST) has risen steadily over the past century, but the overall pattern contains extensive and often uncertain spatial variations, with potentially important effects on regional precipitation. Observations suggest a slowdown of the zonal atmospheric overturning circulation above the tropical Pacific Ocean (the Walker circulation) over the twentieth century. Although this change has been attributed to a muted hydrological cycle forced by global warming, the effect of SST warming patterns has not been explored and quantified. Here we perform experiments using an atmospheric model, and find that SST warming patterns are the main cause of the weakened Walker circulation over the past six decades (1950-2009). The SST trend reconstructed from bucket-sampled SST and night-time marine surface air temperature features a reduced zonal gradient in the tropical Indo-Pacific Ocean, a change consistent with subsurface temperature observations. Model experiments with this trend pattern robustly simulate the observed changes, including the Walker circulation slowdown and the eastward shift of atmospheric convection from the Indonesian maritime continent to the central tropical Pacific. Our results cannot establish whether the observed changes are due to natural variability or anthropogenic global warming, but they do show that the observed slowdown in the Walker circulation is presumably driven by oceanic rather than atmospheric processes.