<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2019-10-25</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000704532</issuerCik>
        <issuerName>Onto Innovation Inc.</issuerName>
        <issuerTradingSymbol>ONTO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001132849</rptOwnerCik>
            <rptOwnerName>ROTH STEVEN R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ONTO INNOVATION INC.</rptOwnerStreet1>
            <rptOwnerStreet2>16 JONSPIN ROAD</rptOwnerStreet2>
            <rptOwnerCity>WILMINGTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01887</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SEE REMARKS</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>No securities beneficially owned</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes></footnotes>

    <remarks>CFO &amp; Senior Vice President, Finance &amp; Administration

On October 25, 2019, the merger (the &quot;Merger&quot;) of PV Equipment Inc., a subsidiary of the Issuer, with and into Rudolph Technologies Inc., pursuant to the Agreement and Plan of Merger, dated as of June 23, 2019, was completed. This report reflects the beneficial ownership of the Reporting Person at the time of completion of the Merger and does not include the securities of the Issuer acquired by the Reporting Person upon the completion of the Merger. The Reporting Person will file a Form 4 reflecting the Reporting Person's acquisition of securities of the Issuer in connection with the completion of the Merger.</remarks>

    <ownerSignature>
        <signatureName>/s/ Robert A. Koch For: Steven R. Roth</signatureName>
        <signatureDate>2019-10-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
