We studied pollen fertility, seed set and cytogenetic characteristics of restorer lines and F1 hybrids of autotetraploid rice. T4002, T4063, T461A x T4002 and T461A x T4063 showed significantly higher pollen fertility and seed set than T4132 and T461A x T4132. Meiotic pairing configurations of T4002, T4063, T4132, T461A x T4002, T461A x T4063 and T461A x T4132 were 0.051 + 19.96II (9.89 rod + 10.07 ring) + 0.01III + + 2.00IV, 0.11I + 19.17II (8.90 rod + 10.37 ring) + 0.09III + 2.26IV + 0.01VI, 1.34I + 9.46II (4.50 rod + 4.96 ring) + 0.80III + 6.02IV + 0.09VI + 0.09VIII, 0.02I + 14.36II (6.44 rod + 7.91 ring) + 0.01III + 4.80IV + 0.01VIII, 0.06I + 17.67II (11.01 rod + 6.67 ring) + 0.06III + 3.10IV + 0.01VI and 1.11I + 11.31II (5.80 rod + 5.51 ring) + 0.41III + 5.63IV + 0.03VI + 0.03VIII, respectively. Configuration 16II + 4IV and 12II + 6IV occurred in the highest frequency among the autotetraploid restorers and hybrids. Meiotic chromosome behaviors were less abnormal in the tetraploids with high seed set than those with low seed set. The hybrids had fewer frequencies of bivalents, univalents, trivalents and multivalents than the restorers, but higher frequency of quatrivalents than the restorers at MI. The frequency of univalents at MI had the most impact on pollen fertility and seed set, i.e., pollen fertility decreased with the increase of univalents. The secondary impact factors were trivalents and multivalents, and bivalents and quatrivalents had no effect on pollen fertility and seed set. The correlative relationship between pollen fertility and cytogenetic behaviors could be utilized to improve seed set in autotetraploidy breeding.