The invention discloses a method for obtaining grape hybrid fruit seeds, and relates to the technical field of fruit breeding. The method comprises the following steps of obtaining grape hybrid seedling fruits from trees, and putting the grape hybrid seedling fruits at a cool and dry place for after-ripening so as to obtain grape seedling fruits; putting the seedling fruits in a pulp refiner to carry out grinding treatment until the seedling fruits are completely grinded into a mixture of seeds, pulps and peels; filtering the mixture to obtain a seed-containing initial extract; washing the initial extract by clear water until the waste water after the washing is clear water, so as to obtain seeds of the grape hybrid fruits; and air-drying the seeds, and carrying out sand storage and stratification on the seeds and wet sand so as to complete the obtaining of the grape hybrid fruit seeds. The method disclosed in the invention has the advantages of being simple, convenient, rapid and effective and yielding twice the result with half the effort.