In the traditional X-ray pulsar Doppler velocimetry approach, a single pulsar only provides the velocity information of spacecraft in the line-of-sight (LOS) direction of a pulsar. Theoretically, we prove that the spacecraft velocity error in any direction can distort the X-ray pulsar profile in orbit around Jupiter. Moreover, using singular value decomposition (SVD), we find that the observability of velocities in both the maximal and middle singular directions is far better than that of the minimal one. Based on theoretical analysis results, we propose a two-dimensional Doppler velocimetry approach using a single X-ray pulsar to provide more velocity information for spacecraft. Firstly, we use SVD to give two well-observable singular directions for velocity estimation. And then, to eliminate duplicate computations in the accumulative process of X-ray pulsar signals, we build the piecewise complete dictionary of accumulated pulsar profiles, which has no identical accumulated pulsar profile. Finally, using the chi-square value of X-ray pulsar sup-profiles as an evaluation standard, we develop the two-level velocity estimation based on dictionary folding (DF) to measure the two-dimensional Doppler velocity. Experimental results demonstrate that compared with the traditional one-dimensional pulsar velocimetry approach, the two-dimensional Doppler velocimetry approach using a single X-ray pulsar provides more velocity information and is more robust to the initial velocity error. The accuracies of velocities in both two singular directions reach 0.3 m/s. In addition, compared with the traditional epoch folding, the elapsed time of the DF reduce by more than 70% and gets 4 min.