Aims. Large samples of protoplanetary disks have been observed in recent ALMA surveys. The gas distributions and velocity structures of most of the disks can still not be imaged at high signal to noise ratios (S/Ns) because of the short integration time per source in these surveys. In this work, we apply the velocity-aligned stacking method to extract more information from molecular-line data of these ALMA surveys and to study the kinematics and disk properties traced by molecular lines. Methods. We re-analyzed the ALMA ¹³CO (3–2) and C¹⁸O (3–2) data of 88 young stellar objects (YSOs) in Lupus with the velocity-aligned stacking method. This method aligns spectra at different positions in a disk based on the projected Keplerian velocities at their positions and then stacks them. This method enhances the S/Ns of molecular-line data and allows us to obtain better detections and to constrain dynamical stellar masses and disk orientations. Results. We obtain ¹³CO detections in 41 disks and C¹⁸O detections in 18 disks with 11 new detections in ¹³CO and 9 new detections in C¹⁸O after applying the method. We estimate the disk orientations and the dynamical masses of the central YSOs from the ¹³CO data. Our estimated dynamical stellar masses correlate with the spectroscopic stellar masses, and in a subsample of 16 sources, where the inclination angles are better constrained, the two masses are in good agreement within the uncertainties and with a mean difference of 0.15 M_⊙. With more detections of fainter disks, our results show that high gas masses derived from the ¹³CO and C¹⁸O lines tend to be associated with high dust masses estimated from the continuum emission. Nevertheless, the scatter is large and is estimated to be 0.9 dex, implying large uncertainties in deriving the disk gas mass from the line fluxes. We find that with such large uncertainties it is expected that there is no correlation between the disk gas mass and the mass accretion rate with the current data. Deeper observations to detect disks with gas masses <10⁻⁵ M_⊙ in molecular lines are needed to investigate the correlation between the disk gas mass and the mass accretion rate.