"To upload a file beyond the feature limit set by ArcGIS Online (1000 features), use feature services. Feature services are a more scalable way to publish features as it supports vector feature querying, visualization, and editing."
Take a look at this official link, from ESRI:
At the moment, I'm uploading a Feature Class with 500k features. I have this feature class in a FGDB and I have used the steps below to upload with ArcMap (found in this link: https://geonet.esri.com/thread/89633):
1) Click on File -> Sign In... (Here you sign into your organizational account)
2) Click on File -> Share As -> Service -> Publish a service
3) As connection choose My Hosted Services (My Account) and as service name use what you want the layer to be called.
4) Under the capabilities tab uncheck "Tiled Mapping" and check "Feature Access"
5) Fill out the Item Description tab
6) Under sharing you can check who is able to see it once published
7) Click Publish in the upper right corner and it will soon show up in your "My Content" on ArcGIS Online